Supported Applications

For more information on environment-modules see Finding Software.

On Mahuika, and Ancillary nodes (both Mahuika and Māui) software packages are provided using 'Lmod' an implementation of Environment Modules with additional features.
A list of available software can be obtained with the module spider command.

On Māui (XC50), software packages are provided using traditional Environment Modules. No modules are loaded by default.
A list of available software can be obtained with the module avail command.

Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.

Available Modules

module load ABAQUS/2020
Links
Licence

ABAQUS is proprietary software.

Access to a valid licence token is required to run ABAQUS.

Institution Faculty Uptime
University of Auckland Faculty of Engineering 98%
University of Waikato 96%

Mass screening of contigs for antimicrobial and virulence genes

Available Modules

module load ABRicate/1.0.0-GCC-11.3.0-Perl-5.34.1
Links

AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates

Available Modules

module load abritamr/1.0.14-gimkl-2022a-Python-3.11.3
Links

Collection of C++ library code designed to augment the C++ standard library.

Available Modules

module load Abseil/20230125.3-GCC-11.3.0
Links

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

Available Modules

module load ABySS/2.2.5-gimpi-2020a
Links

ACTC converts independent triangles into triangle strips or fans.

Available Modules

module load ACTC/1.1-GCCcore-9.2.0
Links

Ssearches for and removes remnant adapter sequences from High-Throughput Sequencing data.

Available Modules

module load AdapterRemoval/2.3.1-GCCcore-7.4.0
Links

AdaptiveCpp (formerly hipSYCL) is a SYCL implementation targeting CPUs and GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP

Available Modules

module load AdaptiveCpp/23.10.0-GCC-12.3.0-CUDA-12.2.2
Links

Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain

Available Modules

module load Advisor/2020_update1
Links

Suite of tools to handle gene annotations in any GTF/GFF format.

Available Modules

module load AGAT/1.0.0-gimkl-2022a-Perl-5.34.1-R-4.2.1
Links

Alignment of sequences with structural variants.

Available Modules

module load AGE/2017-GCC-7.4.0-serial
Links

AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known

Available Modules

module load AlphaFold/2.3.2
Links

AlphaFold2 databases

Available Modules

module load AlphaFold2DB/2022-06
Links

Overrides the MKL internal utility function mkl_serv_intel_cpu_true so that AVX2 optimised kernels will be used, even when running on an AMD CPU.

Available Modules

module load AlwaysIntelMKL/1.0
Links

Collection of tools for genome assembly

Available Modules

module load AMOS/3.1.0-GCC-11.3.0
Links

NCBI Antimicrobial Resistance Gene Finder Plus

Available Modules

module load AMRFinderPlus/3.10.45-GCC-11.3.0
Links

Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. IMPORTANT: This version of Anaconda Python comes with Intel MKL support to speed up certain types of mathematical computations, such as linear algebra or FFT. The module sets MKL_NUM_THREADS=1 to run MKL on a single thread by default, avoiding accidental oversubscription of cores. The number of threads can be increased for large problems, please refer to the Intel MKL documentation for guidance.

Available Modules

module load Anaconda3/2021.05-gimkl-2020a

Warning

Warning: Anaconda is deprecated for license reasons. Please switch to using Miniforge3 for any new environments.

Links

Program for analysing NGS data.

Available Modules

module load angsd/0.935-GCC-9.2.0
Links

Calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes.

Available Modules

module load ANIcalculator/1.0-GCC-11.3.0
Links

Efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes .

Available Modules

module load ANNOVAR/2020Oct01-GCC-9.2.0-Perl-5.30.1
Links

A bundle of computer-aided engineering software including Fluent and CFX.

Available Modules

module load ANSYS/19.2
Links
Licence

ANSYS is proprietary software.

Access to a valid licence token is required to run ANSYS.

Institution Faculty Uptime
University of Auckland Faculty of Engineering 88%
Orbis Diagnostics 100%
Auckland University of Technology Faculty of Engineering 88%
University of Waikato 88%
University of Canterbury 99%
University of Otago 99%

Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.

Available Modules

module load ant/1.10.9-Java-1.8.0_144
Links

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.

Available Modules

module load antiSMASH/5.1.2-gimkl-2020a-Python-3.8.2
Links

ANother Tool for Language Recognition

Available Modules

module load ANTLR/2.7.7-GCC-7.4.0

Warning

Warning: ANTLR/2.7.7-GCC-7.4.0 is old and marked for deletion. If you still need it, then please let us know.

Links

ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.

Available Modules

module load ANTs/2.3.5-gimkl-2020a
Links

Convert various sequence formats to FASTA

Available Modules

module load any2fasta/0.4.2-GCC-11.3.0
Links

AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0

Available Modules

module load AOCC/4.0.0-GCC-11.3.0
Links

Optimized version of FFTW for AMD EPYC family of processors..

Available Modules

module load AOCL-BLIS/4.0-GCC-11.3.0
Links

Optimized version of FFTW for AMD EPYC family of processors.

Available Modules

module load AOCL-FFTW/4.0-gompi-2022a
Links

Optimized version of ScaLAPACK for AMD EPYC family of processors.

Available Modules

module load AOCL-ScaLAPACK/4.0-gompi-2022a
Links

Apptainer is a portable application stack packaging and runtime utility.

Available Modules

module load Apptainer/1.2.5
Links

Apache Portable Runtime (APR) libraries.

Available Modules

module load APR/1.6.5
Links

Apache Portable Runtime (APR) util libraries.

Available Modules

module load APR-util/1.6.1

Warning

Warning: APR-util/1.6.1 is old and marked for deletion. If you still need it, then please let us know.

Links

Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.

Available Modules

module load argtable/2.13-GCC-11.3.0
Links

aria2 is a lightweight multi-protocol & multi-source command-line download utility.

Available Modules

module load aria2/1.36.0-GCCcore-11.3.0
Links

Antimicrobial Resistance Identification By Assembly

Available Modules

module load ARIBA/2.14.6-gimkl-2022a-Python-3.10.5
Links

C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use.

Available Modules

module load Armadillo/10.5.3-gimkl-2020a
Links

ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

Available Modules

module load arpack-ng/3.6.3-intel-2017a

Warning

Links

Apache Arrow, a cross-language development platform for in-memory data.

Available Modules

module load Arrow/8.0.0-GCCcore-11.3.0
Links

a pArallel Server for Adaptive GeoInformation

Available Modules

module load ASAGI/20240327-foss-2023a
Links

IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.

Available Modules

module load Aspera-CLI/3.9.6.1467.159c5b1
Links

AT-SPI 2 toolkit bridge

Available Modules

module load at-spi2-atk/2.38.0-GCCcore-9.2.0
Links

Assistive Technology Service Provider Interface.

Available Modules

module load at-spi2-core/2.38.0-GCCcore-9.2.0
Links

ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications.

Available Modules

module load ATK/2.36.0-GCCcore-9.2.0
Links

Commands for Manipulating Filesystem Extended Attributes

Available Modules

module load attr/2.5.1-GCCcore-9.2.0
Links

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

Available Modules

module load AUGUSTUS/3.4.0-gimkl-2020a
Links

A collection of more than 500 macros for GNU Autoconf

Available Modules

module load Autoconf-archive/2023.02.20
Links

OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units.

Available Modules

module load AutoDock-GPU/1.5.3-GCC-11.3.0-CUDA-11.6.2
Links

AutoDock Vina is an open-source program for doing molecular docking.

Available Modules

module load AutoDock_Vina/1.1.2_linux_x86
Links

Java Development Kit (JDK), and a compliant implementation of the Java Standard Edition (SE) specification.

Available Modules

module load azul-zulu/17.36.19-jdk-17.0.4.1
Links

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

Available Modules

module load BamTools/2.5.1-gimkl-2018b
Links

Repository that contains several programs that perform operations on SAM/BAM files.

Available Modules

module load bamUtil/1.0.15
Links

Bandage is a program for visualising de novo assembly graphs

Available Modules

module load Bandage/0.8.1_Centos
Links

Barrnap predicts the location of ribosomal RNA genes in genomes.

Available Modules

module load barrnap/0.9-GCC-9.2.0
Links

Basilisk is a Free Software program for the solution of partial differential equations on adaptive Cartesian meshes.

Available Modules

module load Basilisk/20200620-gimpi-2020
Links

Program for inference of recent immigration rates between populations using unlinked multilocus genotypes

Available Modules

module load BayesAss/3.0.4-GCC-9.2.0
Links

Identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.

Available Modules

module load BayeScan/2.1-GCCcore-7.4.0
Links

Genome-Wide Scan for Adaptive Differentiation and Association Analysis with population-specific covariables

Available Modules

module load BayPass/2.31-intel-2022a
Links

Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.

Available Modules

module load Bazel/3.4.1-GCCcore-9.2.0

Warning

Warning: Bazel/3.7.2-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

BBMap short read aligner, and other bioinformatic tools.

Available Modules

module load BBMap/38.95-gimkl-2020a
Links

Manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.

Available Modules

module load BCFtools/1.12-GCC-9.2.0

Warning

Links

Converts per cycle binary data output by Illumina sequencers containing basecall files and quality scores to per read FASTQ files

Available Modules

module load BCL-Convert/4.0.3

Warning

Links

bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.

Available Modules

module load bcl2fastq2/2.20.0-gimkl-2018b
Links

Package for phasing genotypes and for imputing ungenotyped markers.

Available Modules

module load Beagle/5.0-12Jul19.0df
Links

beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

Available Modules

module load beagle-lib/3.0.1-gimkl-2017a

Warning

Links

Bayesian MCMC phylogenetic analysis of molecular sequences for reconstructing phylogenies and testing evolutionary hypotheses.

Available Modules

module load BEAST/2.6.6
Links

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.

Available Modules

module load BEDOPS/2.4.41-gimkl-2022a
Links

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.

Available Modules

module load BEDTools/2.31.1-GCC-12.3.0
Links

BEEF is a library implementing the Bayesian Error Estimation Functional, a description of which can be found here: http://dx.doi.org/10.1103/PhysRevB.85.235149

Available Modules

module load BEEF/0.1.1-r16-intel-2020a
Links

Bam Error Stats Tool (best): analysis of error types in aligned reads

Available Modules

module load best/0.1.0
Links

Collection of code for Bayesian genomic cline analyses.

Available Modules

module load BGC-Bayesian-genomic-clines/1.03-gompi-2023a
Links

Highly parallel construction, indexing and querying of colored and compacted de Bruijn graphs.

Available Modules

module load Bifrost/1.0.4-GCC-9.2.0

Warning

Links

Constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs).

Available Modules

module load BiG-SCAPE/1.1.5-gimkl-2022a-Python-3.11.3
Links

binutils: GNU binary utilities

Available Modules

module load binutils/2.26-GCCcore-5.4.0
Links

Read BigWig and BigBed genome feature databases

Available Modules

module load Bio-DB-BigFile/1.07-GCC-9.2.0-Perl-5.30.1-mt
Links

Read files using HTSlib including BAM/CRAM, Tabix and BCF database files

Available Modules

module load Bio-DB-HTS/3.01-GCC-11.3.0-Perl-5.34.1
Links

An extension to awk, adding the support of several common biological data formats

Available Modules

module load bioawk/1.0
Links

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

Available Modules

module load BioPP/2.4.1-GCC-9.2.0
Links

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Available Modules

module load Bismark/0.22.3-gimkl-2018b
Links

Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

Available Modules

module load Bison/3.0.4-GCC-5.4.0
Links

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

Available Modules

module load BLAST/2.9.0-gimkl-2018b
Links

BLAST databases downloaded from NCBI.

Available Modules

module load BLASTDB/2024-07
Links

BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.

Available Modules

module load BLAT/3.5-gimkl-2018b

Warning

Warning: BLAT/3.5-gimkl-2018b is old and marked for deletion. Please select a more recent version (try 'module spider BLAT') or let us know that you still need it.

Links

Blender provides a pipeline for 3D modeling, rigging, animation, simulation, rendering, compositing, motion tracking, video editing and 2D animation. This particular build of Blender provides a Python package 'bpy' rather than the stand-alone application.

Available Modules

module load BlenderPy/2.93.1-gimkl-2020a-Python-3.9.5

Warning

Warning: BlenderPy/2.93.1-gimkl-2020a-Python-3.9.5 is old and marked for deletion. If you still need it, then please let us know.

Links

BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.

Available Modules

module load BLIS/0.9.0-GCC-11.3.0
Links

The BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis

Available Modules

module load BOLT-LMM/2.4
Links

Boost provides free peer-reviewed portable C++ source libraries.

Available Modules

module load Boost/1.76.0-intel-2022a
Links

Ultrafast, memory-efficient short read aligner.

Available Modules

module load Bowtie/0.12.8
Links

Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Available Modules

module load Bowtie2/2.4.1-GCC-9.2.0
Links

A platform for running big bioinformatics jobs that consist of a series of processing stages

Available Modules

module load Bpipe/0.9.9.8

Warning

Warning: Bpipe/0.9.9.8 is old and marked for deletion. If you still need it, then please let us know.

Links

Hghly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Available Modules

module load Bracken/2.6.0-GCCcore-9.2.0

Warning

Links

BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.

Available Modules

module load BRAKER/2.1.6-gimkl-2020a-Perl-5.30.1-Python-3.8.2

Warning

Links

Genome-wide detection of structural variants from next generation paired-end sequencing reads.

Available Modules

module load BreakDancer/1.4.5-gimkl-2017a.lua
Links

Nucleotide-resolution analysis of structural variants

Available Modules

module load BreakSeq2/2.2-gimkl-2018b-Python-2.7.16

Warning

Warning: BreakSeq2/2.2-gimkl-2018b-Python-2.7.16 is old and marked for deletion. If you still need it, then please let us know.

Links

breseq is a computational pipeline for the analysis of short-read re-sequencing data

Available Modules

module load breseq/0.35.4-gimkl-2020a-R-4.0.1

Warning

Links

bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects.

Available Modules

module load bsddb3/6.2.6-gimkl-2018b-Python-2.7.16

Warning

Warning: bsddb3/6.2.6-gimkl-2018b-Python-2.7.16 is old and marked for deletion. If you still need it, then please let us know.

Links

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

Available Modules

module load BUSCO/4.0.5-gimkl-2020a
Links

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.

Available Modules

module load BWA/0.7.15-gimkl-2017a

Warning

Links

bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

Available Modules

module load bzip2/1.0.8-GCCcore-9.2.0
Links

c-ares is a C library for asynchronous DNS requests (including name resolves)

Available Modules

module load c-ares/1.18.1-GCCcore-11.3.0
Links

Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB

Available Modules

module load cairo/1.16.0-GCCcore-9.2.0
Links

Sequence assembler designed for high-noise single-molecule sequencing.

Available Modules

module load Canu/2.2-GCC-11.3.0
Links

Fast data interchange format and capability-based RPC system.

Available Modules

module load CapnProto/0.8.0-GCCcore-9.2.0
Links

A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch)

Available Modules

module load Catch2/2.13.4

Warning

Warning: Catch2/2.13.4 is old and marked for deletion. If you still need it, then please let us know.

Links

Clozure CL (often called CCL for short) is a free Common Lisp implementation

Available Modules

module load CCL/1.12-GCCcore-9.2.0

Warning

Warning: CCL/1.12-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

Available Modules

module load CD-HIT/4.8.1-GCC-11.3.0
Links

Fasta file indexing and retrival tool

Available Modules

module load cdbfasta/0.99-GCC-11.3.0
Links

CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

Available Modules

module load CDO/1.9.8-gimpi-2020a
Links

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

Available Modules

module load CellRanger/6.1.2
Links

Classifier for metagenomic sequences

Available Modules

module load Centrifuge/1.0.4.1-GCC-12.3.0
Links

C++11 serialization library

Available Modules

module load Cereal/1.3.0
Links

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

Available Modules

module load CFITSIO/3.45-GCCcore-7.4.0
Links

The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.

Available Modules

module load CGAL/4.13-GCCcore-7.4.0
Links

Nvidia and AMD GPU utility for SeisSol.

Available Modules

module load chainforge/0.0.3-foss-2023a-Python-3.11.6
Links

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.

Available Modules

module load CheckM/1.2.1-gimkl-2022a-Python-3.10.5
Links

Rapid assessment of genome bin quality using machine learning

Available Modules

module load CheckM2/1.0.1-Miniconda3
Links

Assess the quality of metagenome-assembled viral genomes.

Available Modules

module load CheckV/0.6.0-gimkl-2020a-Python-3.8.2

Warning

Links

A complete suite for gene-by-gene schema creation and strain identification..

Available Modules

module load chewBBACA/3.1.2-gimkl-2022a-Python-3.11.3
Links

Rust implementation of NanoFilt+NanoLyse

Available Modules

module load chopper/0.5.0-GCC-11.3.0
Links

A tool to circularize genome assemblies

Available Modules

module load Circlator/1.5.5-gimkl-2022a-Python-3.10.5
Links

Package for visualizing data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.

Available Modules

module load Circos/0.69-9-GCC-9.2.0
Links

Syumphonizing pileup and full-alignment for high-performance long-read variant calling.

Available Modules

module load Clair3/0.1.12-Miniconda3
Links

C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.

Available Modules

module load Clang/17.0.6-GCC-12.3.0-CUDA-12.2.2
Links

Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms

Available Modules

module load Clustal-Omega/1.2.4-GCC-11.3.0
Links

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.

Available Modules

module load ClustalW2/2.1-gimkl-2017a

Warning

Warning: ClustalW2/2.1-gimkl-2017a was built with an old compiler and will soon be removed. Please switch to using ClustalW2/2.1-GCC-11.3.0 instead, or even better switch to newer tools such as MUSCLE or MAFFT for DNA alignments, or Clustal-Omega for protein alignments

Links

CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

Available Modules

module load CMake/3.22.1
Links

Copy Number Variation discovery and genotyping from depth of read mapping.

Available Modules

module load CNVnator/0.4-GCC-7.4.0
Links

Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped read

Available Modules

module load CNVpytor/1.0-gimkl-2020a-Python-3.8.2
Links

code-server for OpenOnDemand

Available Modules

module load code-server/4.92.2
Links

faster and more accurate reimplementation of BUSCO.

Available Modules

module load compleasm/0.2.6-gimkl-2022a
Links

COMSOL is a multiphysics solver that provides a unified workflow for electrical, mechanical, fluid, and chemical applications.

Available Modules

module load COMSOL/5.6
Links
Licence

COMSOL is proprietary software.

Access to a valid licence token is required to run COMSOL.

Institution Faculty Uptime
University of Auckland Physics 98%
Auckland Bioengineering Institute Implantable devices group 98%
University of Auckland Faculty of Engineering 98%
University of Auckland Deptartment of Engineering Science 98%
University of Auckland Deptartment of Engineering Science 98%
University of Otago 99%
University of Canterbury 100%

Program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

Available Modules

module load CONCOCT/1.1.0-gimkl-2020a-Python-3.8.2
Links

Clusters contigs and counts reads from de novo assembled transcriptomes.

Available Modules

module load Corset/1.09-GCC-9.2.0

Warning

Warning: Corset/1.09-GCC-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

DNA read coverage and relative abundance calculator focused on metagenomics applications

Available Modules

module load CoverM/0.7.0-GCC-12.3.0
Links

CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

Available Modules

module load CP2K/8.2-intel-2022a-PLUMED-2.7.2
Links

The CPMD code is a parallelized plane wave / pseudopotential implementation of DFT, particularly designed for ab-initio molecular dynamics.

Available Modules

module load CPMD/4.3-foss-2023a
Links

C++ port of the JUnit framework for unit testing.

Available Modules

module load CppUnit/1.13.2-GCCcore-7.4.0

Warning

Warning: CppUnit/1.15.1-GCCcore-11.3.0 is old and marked for deletion. If you still need it, then please let us know.

Links

A tool for quick quality assessment of cram and bam files, intended for long read sequencing

Available Modules

module load CRAMINO/0.9.7-GCC-11.3.0
Links

Workflow Management System geared towards scientific workflows.

Available Modules

module load cromwell/84-Java-1.8.0_144
Links

Ctags generates an index (or tag) file of language objects found in source files that allows these items to be quickly and easily located by a text editor or other utility.

Available Modules

module load ctags/5.8

Warning

Warning: ctags/5.8 is old and marked for deletion. If you still need it, then please let us know.

Links

ctffind is a program for finding CTFs of electron micrographs

Available Modules

module load ctffind/4.1.10
Links

C++ Thread Pool Library

Available Modules

module load CTPL/0.0.2

Warning

Warning: CTPL/0.0.2 is old and marked for deletion. If you still need it, then please let us know.

Links

Cube general purpose C++ library component and command-line tools.

Available Modules

module load CubeLib/4.4.4-GCCcore-9.2.0
Links

Cube high-performance C writer library component.

Available Modules

module load CubeWriter/4.5-GCCcore-9.2.0
Links

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

Available Modules

module load CUDA/11.0.2
Links

The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.

Available Modules

module load cuDNN/7.6.4.38-CUDA-10.1.243
Links

Transcript assembly, differential expression, and differential regulation for RNA-Seq

Available Modules

module load Cufflinks/2.2.1-gimkl-2017a
Links

Automated testing framework for C.

Available Modules

module load CUnit/2.1-3-GCCcore-9.2.0

Warning

Warning: CUnit/2.1-3-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.

Available Modules

module load cURL/8.3.0-GCCcore-12.3.0
Links

cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.

Available Modules

module load cutadapt/1.16-gimkl-2018b-Python-3.7.3
Links

Fast and scalable long-read-based SV detection

Available Modules

module load cuteSV/2.0.2-gimkl-2020a-Python-3.8.2
Links

Common Workflow Language tool description reference implementation

Available Modules

module load cwltool/3.0.20200317203547-gimkl-2020a-Python-3.8.2

Warning

Warning: cwltool/3.0.20200317203547-gimkl-2020a-Python-3.8.2 is old and marked for deletion. If you still need it, then please let us know.

Links

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Available Modules

module load Cytoscape/2.7.0

Warning

Links

cython + htslib == fast VCF and BCF processing

Available Modules

module load cyvcf2/0.30.11-gimkl-2020a-Python-3.8.2
Links

D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.

Available Modules

module load D-Genies/1.5.0-gimkl-2022a-Python-3.11.3
Links

Diffusion Approximation for Demographic Inference

Available Modules

module load dadi/2.3.0-gimkl-2022a-Python-3.11.3
Links

Tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.

Available Modules

module load DaliLite/5.0-iimpi-2020a

Warning

Warning: DaliLite/5.0-iimpi-2020a is old and marked for deletion. If you still need it, then please let us know.

Links

de novo transcriptome annotator..

Available Modules

module load dammit/1.2

Warning

Warning: dammit/1.2 is old and marked for deletion. If you still need it, then please let us know.

Links

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

Available Modules

module load DAS_Tool/1.1.5-gimkl-2022a-R-4.2.1
Links

Tool to gather data from across NCBI databases

Available Modules

module load datasets/15.29.0
Links

Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.

Available Modules

module load DB/6.2.23-GCCcore-7.4.0
Links

D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed.

Available Modules

module load DBus/1.13.8-GCCcore-7.4.0
Links

A tool that can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets.

Available Modules

module load DeconSeq/0.4.3
Links

Efficient method for 3D markerless pose estimation based on transfer learning with deep neural networks.

Available Modules

module load DeepLabCut/2.3.5
Links

Available Modules

module load DeePMD-kit/2.1.1
Links

deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

Available Modules

module load deepTools/3.2.1-gimkl-2018b-Python-3.7.3
Links

Integrated simulation of sediment transport and morphology, waves, water quality and ecology.

Available Modules

module load Delft3D/141732-intel-2022a
Links

3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments

Available Modules

module load Delft3D_FM/68673-intel-2020a
Links

Structural variant discovery by integrated paired-end and split-read analysis

Available Modules

module load Delly/1.1.3
Links

R functions that simplify and expedite common tasks in package development.

Available Modules

module load devtools/2.4.4-gimkl-2022a-R-4.2.1
Links

Generally Applicable Atomic-Charge Dependent London Dispersion Correction.

Available Modules

module load DFT-D4/3.5.0-foss-2023a
Links

Sequence aligner for protein and translated DNA searches

Available Modules

module load DIAMOND/2.1.9-GCC-11.3.0
Links

Assembler suitable for large genomes based on Illumina reads of length 250 or longer.

Available Modules

module load DISCOVARdenovo/52488

Warning

Warning: DISCOVARdenovo/52488 is old and marked for deletion. If you still need it, then please let us know.

Links

High-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.

Available Modules

module load Dorado/0.3.2
Links

Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.

Available Modules

module load double-conversion/3.2.1-GCC-11.3.0

Warning

Warning: double-conversion/3.2.1-GCC-11.3.0 is old and marked for deletion. Please select a more recent version (try 'module spider double-conversion') or let us know that you still need it.

Links

Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.

Available Modules

module load Doxygen/1.8.17-GCCcore-9.2.0
Links

Tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs..

Available Modules

module load DRAM/1.3.5-Miniconda3
Links

Rapid and accurate comparison and de-replication of microbial genomes

Available Modules

module load drep/2.3.2-gimkl-2018b-Python-3.7.3
Links

Fast calculation of the ABBA-BABA statistics across many populations/species

Available Modules

module load Dsuite/20210718-intel-compilers-2022.0.2
Links

DTCMP Library provides pre-defined and user-defined comparison operations to compare the values of two items which can be arbitrary MPI datatypes.

Available Modules

module load dtcmp/1.1.3-gimpi-2020a
Links

uphold your DUP and DEL calls

Available Modules

module load duphold/0.2.3
Links

Range of tools to support operations on Duplex Sequencing read pairs.

Available Modules

module load duplex-tools/0.2.20-gimkl-2022a-Python-3.10.5
Links

easi is a library for the Easy Initialization of models in three (or less or more) dimensional domains.

Available Modules

module load easi/1.3.0-foss-2023a
Links

Available Modules

module load EasyBuild/4.7
Links

ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).

Available Modules

module load ecCodes/2.17.0-gimpi-2020a
Links

Standalone versatile serotyping module for Escherichia coli..

Available Modules

module load ectyper/1.0.0-gimkl-2022a-Python-3.10.5
Links

Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.

Available Modules

module load edlib/1.3.8.post2-gimkl-2020a-Python-3.8.2
Links

A suite of tools to conduct metabarcoding analyses targeting any group of organisms. Includes utilities for preprocessing raw data and building your own custom reference database.

Available Modules

module load eDNA/2021.11-gimkl-2020a-Python-3.8.2
Links

Automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.

Available Modules

module load EDTA/2.1.0
Links

Tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments

Available Modules

module load eggnog-mapper/2.0.1b-gimkl-2020a-Python-2.7.18
Links

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

Available Modules

module load Eigen/3.3.9
Links

The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

Available Modules

module load EIGENSOFT/7.2.1-gimkl-2018b
Links

Eigenvalue SoLvers for Petaflop-Applications .

Available Modules

module load ELPA/2023.11.001-foss-2023a
Links

Greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes

Available Modules

module load EMAN2/2.99.47-gpu
Links

EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.

Available Modules

module load EMBOSS/6.6.0-gimkl-2020a
Links

Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels.

Available Modules

module load Embree/3.5.1-GCCcore-7.4.0
Links

Tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly

Available Modules

module load emmtyper/0.2.0-gimkl-2022a-Python-3.11.3
Links

R package for integrated construction of Ecological Niche Models.

Available Modules

module load ENMTML/2021-06-24-gimkl-2020a-R-4.1.0

Warning

Warning: ENMTML/2021-06-24-gimkl-2020a-R-4.1.0 is old and marked for deletion. If you still need it, then please let us know.

Links

C++ header-only library for numerical optimization

Available Modules

module load ensmallen/2.17.0-gimkl-2020a
Links

an advanced method for accessing the NCBI's set of interconnected databases such as publication, sequence, structure, gene, variation, expression, etc.

Available Modules

module load entrez-direct/13.3
Links

The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models.

Available Modules

module load ESMF/7.1.0r-intel-2018b
Links

A Python framework for the analysis and visualization of phylogenetic trees

Available Modules

module load ETE/3.1.1-gimkl-2018b-Python-3.7.3
Links

Completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes. Also condatains smetana, carveme and memote .

Available Modules

module load EukRep-EukCC/0.6.7-2.1.0-Miniconda3
Links

Bayesian tree inference, particularly suitable for large-scale analyses.

Available Modules

module load ExaBayes/1.5.1-gimpi-2020a
Links

Exascale Maximum Likelihood for phylogenetic inference using MPI.

Available Modules

module load ExaML/3.0.22-gimkl-2020a
Links

Generic tool for pairwise sequence comparison

Available Modules

module load exonerate/2.4.0-GCC-9.2.0
Links

Tool for estimating repeat sizes

Available Modules

module load ExpansionHunter/5.0.0
Links

Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)

Available Modules

module load expat/2.2.9-GCCcore-9.2.0
Links

Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches

Available Modules

module load Extrae/3.8.3-intel-2020a

Warning

Warning: Extrae/3.8.3-intel-2020a is old and marked for deletion. If you still need it, then please let us know.

Links

Falcon: a set of tools for fast aligning long reads for consensus and assembly

Available Modules

module load FALCON/1.8.8-gimkl-2020a-Python-2.7.18
Links

Tool for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).

Available Modules

module load FastANI/1.33-intel-2020a
Links

FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.

Available Modules

module load FastME/2.1.6.1-gimkl-2018b
Links

A tool designed to provide fast all-in-one preprocessing for FastQ files.

Available Modules

module load fastp/0.20.0-GCCcore-7.4.0
Links

A collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.

Available Modules

module load fastq-tools/0.8-gimkl-2017a

Warning

Warning: fastq-tools/0.8-gimkl-2017a is old and will soon be removed. Please let us know if you would like a new version of fastq-tools to be installed.

Links

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

Available Modules

module load FastQ_Screen/0.15.1-GCC-9.2.0-Perl-5.30.1
Links

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

Available Modules

module load FastQC/0.12.1
Links

fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.

Available Modules

module load fastStructure/1.0-gimkl-2020a-Python-2.7.18
Links

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

Available Modules

module load FastTree/2.1.11-GCC-12.3.0
Links

Tools for Short-Reads FASTA/FASTQ files preprocessing.

Available Modules

module load FASTX-Toolkit/0.0.14-GCC-11.3.0
Links

Format converting tool for genotype Data.

Available Modules

module load fcGENE/1.0.7

Warning

Warning: fcGENE/1.0.7 is old and marked for deletion. If you still need it, then please let us know.

Links

FCM Build - A powerful build system for modern Fortran software applications. FCM Version Control - Wrappers to the Subversion version control system, usage conventions and processes for scientific software development.

Available Modules

module load FCM/2019.09.0-GCC-12.3.0
Links

Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.

Available Modules

module load FDS/6.7.5-1526-intel-2020a

Warning

Links

A complete, cross-platform solution to record, convert and stream audio and video.

Available Modules

module load FFmpeg/5.1.1-GCC-11.3.0
Links

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

Available Modules

module load FFTW/3.3.10-GCC-12.3.0
Links

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

Available Modules

module load FFTW.MPI/3.3.10-gompi-2023a
Links

A set of tools to analyze genomic data with a focus on Next Generation Sequencing.

Available Modules

module load fgbio/2.0.2

Warning

Warning: fgbio/2.0.2 is old and marked for deletion. If you still need it, then please let us know.

Links

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.

Available Modules

module load FIGARO/1.1.2-gimkl-2022a-Python-3.11.3
Links

A Perl version of the rename utility, with support for regular expressions.

Available Modules

module load File-Rename/1.13-GCC-9.2.0
Links

Tool for filtering long reads by quality.

Available Modules

module load Filtlong/0.2.0
Links

Identifies the FimH type in total or partial sequenced isolates of E. coli..

Available Modules

module load FimTyper/1.0.1-GCC-11.3.0-Perl-5.34.1

Warning

Warning: FimTyper/1.0.1-GCC-11.3.0-Perl-5.34.1 is old and marked for deletion. If you still need it, then please let us know.

Links

A package for population structure inference from RAD-seq data

Available Modules

module load fineRADstructure/0.3.2r109-GCCcore-7.4.0

Warning

Links

Population assignment using large numbers of densely sampled genomes, including both SNP chips and sequence dat

Available Modules

module load fineSTRUCTURE/4.1.1-gimkl-2022a-Perl-5.34.1
Links

FlatBuffers: Memory Efficient Serialization Library

Available Modules

module load flatbuffers/2.0.0-GCCcore-9.2.0

Warning

Warning: flatbuffers/2.0.0-GCCcore-9.2.0 is old and marked for deletion. Please select a more recent version (try 'module spider flatbuffers') or let us know that you still need it.

Links

Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

Available Modules

module load flex/2.6.0-GCC-5.4.0
Links

FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.

Available Modules

module load FlexiBLAS/3.3.1-GCC-12.3.0
Links

FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.

Available Modules

module load FLTK/1.3.5-GCCcore-9.2.0
Links

Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.

Available Modules

module load Flye/2.9.5-foss-2023a-Python-3.11.6
Links

Tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data

Available Modules

module load fmlrc/1.0.0-GCC-9.2.0

Warning

Warning: fmlrc/1.0.0-GCC-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Formatting library providing a fast and safe alternative to C stdio and C++ iostreams.

Available Modules

module load fmt/8.0.1
Links

Fontconfig is a library designed to provide system-wide font configuration, customization and application access.

Available Modules

module load fontconfig/2.14.2-GCCcore-12.3.0
Links

Arm Forge combines Arm DDT, the leading debugger for time-saving high performance application debugging, and Arm MAP, the trusted performance profiler for invaluable optimization advice.

Available Modules

module load forge/21.1.3.lua
Links

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

Available Modules

module load foss/2022a
Links

FragGeneScan is an application for finding (fragmented) genes in short reads.

Available Modules

module load FragGeneScan/1.31-gimkl-2018b
Links

Genetic variant detector designed to find polymorphisms smaller than the length of a short-read sequencing alignment.

Available Modules

module load FreeBayes/1.3.2-GCC-9.2.0
Links

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.

Available Modules

module load FreeSurfer/7.2.0-centos7_x86_64
Links

FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.

Available Modules

module load freetype/2.11.1-GCCcore-11.3.0
Links

FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

Available Modules

module load FreeXL/1.0.2-gimkl-2017a
Links

Free Implementation of the Unicode Bidirectional Algorithm.

Available Modules

module load FriBidi/1.0.12-GCC-12.3.0
Links

FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications.

Available Modules

module load FTGL/2.1.3-rc5-GCCcore-7.4.0
Links

funcX is a distributed Function as a Service (FaaS) platform that enables flexible, scalable, and high performance remote function execution. Unlike centralized FaaS platforms, funcX allows users to execute functions on heterogeneous remote computers, from laptops to campus clusters, clouds, and supercomputers. A funcX endpoint is a persistent service launched by the user on a compute system to serve as a conduit for executing functions on that computer.

Available Modules

module load funcx-endpoint/1.0.2-gimkl-2020a-Python-3.9.9

Warning

Links

Extract sequences from a fastx (fasta or fastq) file given a subsequence.

Available Modules

module load fxtract/2.4-GCC-11.3.0
Links

Library contains GRIB2 encoder/decoder ('C' version).

Available Modules

module load g2clib/1.6.0-GCC-12.3.0
Links

Library contains GRIB2 encoder/decoder and search/indexing routines.

Available Modules

module load g2lib/3.2.0-GCC-12.3.0
Links

A reference implementation of the GA4GH API

Available Modules

module load ga4gh/0.3.6-gimkl-2020a-Python-2.7.18

Warning

Warning: ga4gh/0.3.6-gimkl-2020a-Python-2.7.18 is old and marked for deletion. If you still need it, then please let us know.

Links

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

Available Modules

module load GATK/3.8-1
Links

Available Modules

module load Gaussian/09-C
Links
Licence

Gaussian is proprietary software.

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).

Available Modules

module load GCC/5.4.0
Links

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).

Available Modules

module load GCCcore/5.4.0
Links

Libraries and tools for interacting with Google Cloud products and services.

Available Modules

module load gcloud/485.0.0
Links

Interface to Gd Graphics Library

Available Modules

module load GD/2.76-GCC-11.3.0-Perl-5.34.1
Links

GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for data translation and processing. NOTE: The GDAL IO cache by default uses 5% of total memory. This seems not necessary. This module sets GDAL_CACHEMAX=256 (256MB), which should have no performance impact. Feel free to change if necessary, using 'export GDAL_CACHEMAX=xxx' (in your job script) after loading the GDAL module.

Available Modules

module load GDAL/3.0.4-gimkl-2020a.lua
Links

The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

Available Modules

module load Gdk-Pixbuf/2.42.8-GCC-11.3.0
Links

Available Modules

module load geany/1
Links

Genome-wide Efficient Mixed Model Association

Available Modules

module load GEMMA/0.98.5-GCC-12.3.0
Links

GPU-GEMM generator for the Discontinuous Galerkin method.

Available Modules

module load gemmforge/0.0.207-foss-2023a-Python-3.11.6
Links

Eukaryotic gene prediction suite with automatic training

Available Modules

module load GeneMark-ES/4.71-GCC-11.3.0
Links

GenomeThreader is a software tool to compute gene structure predictions.

Available Modules

module load GenomeThreader/1.7.3-Linux_x86_64-64bit
Links

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations.

Available Modules

module load genometools/1.6.1-GCCcore-7.4.0
Links

Generates circular genome representations for complete, draft, and multiple bacterial and archaeal genomes.

Available Modules

module load GenoVi/0.2.16-Miniconda3
Links

GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)

Available Modules

module load GEOS/3.11.3-GCC-12.3.0
Links

Toolkit to assemble organelle genome from genomic skimming data.

Available Modules

module load GetOrganelle/1.7.7.0-gimkl-2022a
Links

GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation

Available Modules

module load gettext/0.19.8.1
Links

single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

Available Modules

module load gfastats/1.3.6-GCC-11.3.0
Links

GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

Available Modules

module load gffread/0.12.7-GCC-11.3.0
Links

giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.

Available Modules

module load giflib/5.2.1-GCCcore-9.2.0
Links

GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL

Available Modules

module load gimkl/2018b
Links

GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.

Available Modules

module load gimpi/2018b
Links

Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

Available Modules

module load git/2.23.3
Links

GLib is one of the base libraries of the GTK+ project

Available Modules

module load GLib/2.53.7-GCCcore-7.4.0
Links

C++ bindings for Glib

Available Modules

module load GLibmm/2.49.7-GCCcore-9.2.0.lua
Links

Gene finder based on a Generalized Hidden Markov Model.

Available Modules

module load GlimmerHMM/3.0.4c-GCC-9.2.0
Links

OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.

Available Modules

module load GLM/0.9.9.8
Links

Client for the Globus Flows service.

Available Modules

module load globus-automate-client/0.16.1.post1-gimkl-2022a
Links

Globus Compute is a distributed Function as a Service (FaaS) platform that enables flexible, scalable, and high performance remote function execution. Unlike centralized FaaS platforms, Globus Compute allows users to execute functions on heterogeneous remote computers, from laptops to campus clusters, clouds, and supercomputers. A Globus Compute endpoint is a persistent service launched by the user on a compute system to serve as a conduit for executing functions on that computer.

Available Modules

module load globus-compute-endpoint/2.24.0-gimkl-2022a-Python-3.10.5
Links

GNU Linear Programming Kit is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems.

Available Modules

module load GLPK/5.0-GCCcore-11.3.0
Links

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program

Available Modules

module load GMAP-GSNAP/2021-12-17-GCC-11.3.0
Links

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

Available Modules

module load GMP/6.2.1-GCCcore-12.3.0
Links

Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor..

Available Modules

module load gmsh/2.0.2-Miniconda3
Links

Portable interactive, function plotting utility

Available Modules

module load gnuplot/5.4.2-GCC-7.4.0
Links

An open source programming language

Available Modules

module load Go/1.11.5

Warning

Links

GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.

Available Modules

module load GObject-Introspection/1.72.0-GCC-11.3.0

Warning

Warning: GObject-Introspection/1.72.0-GCC-11.3.0 is old and marked for deletion. If you still need it, then please let us know.

Links

A genetic algorithm for docking flexible ligands into protein binding sites

Available Modules

module load GOLD/2020

Warning

Links
Licence

GOLD is proprietary software.

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.

Available Modules

module load gompi/2022a
Links

An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed.

Available Modules

module load google-sparsehash/2.0.3-gimkl-2018b
Links

Google's C++ test framework

Available Modules

module load googletest/1.10.0-GCCcore-9.2.0
Links

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.

Available Modules

module load GPAW/24.1.0-foss-2023a
Links

GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.

Available Modules

module load gperf/3.1-GCCcore-7.4.0
Links

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.

Available Modules

module load Graphviz/2.42.2-GCC-9.2.0
Links

The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization

Available Modules

module load GRASS/7.6.1-gimkl-2018b-Python-2.7.16
Links

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

Available Modules

module load GRIDSS/2.13.2-gimkl-2020a
Links

Command line tool for Google Drive.

Available Modules

module load grive2/0.5.1-GCCcore-9.2.0

Warning

Warning: grive2/0.5.1-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI binaries.

Available Modules

module load GROMACS/2020.5-intel-2020a-cuda-11.0.2-hybrid
Links

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.

Available Modules

module load GSL/2.7-GCC-12.3.0
Links

Tool to sort genomic files according to a genomefile.

Available Modules

module load gsort/0.1.4

Warning

Warning: gsort/0.1.4 is old and marked for deletion. If you still need it, then please let us know.

Links

GStreamer plug-ins and elements.

Available Modules

module load GST-plugins-base/1.16.2-GCC-9.2.0
Links

library for constructing graphs of media-handling components..

Available Modules

module load GStreamer/1.16.2-GCC-9.2.0
Links

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Available Modules

module load GTDB-Tk/2.1.0-gimkl-2020a-Python-3.9.9
Links

GTK+ is the primary library used to construct user interfaces in GNOME.

Available Modules

module load GTK+/3.24.23-GCC-9.2.0
Links

GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.

Available Modules

module load GTS/121130-GCCcore-7.4.0
Links

Genealogies Unbiased By recomBinations In Nucleotide Sequences

Available Modules

module load Gubbins/3.2.2-gimkl-2022a-Python-3.10.5
Links

Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation.

Available Modules

module load GUSHR/2020-09-28-gimkl-2022a-Python-3.11.3
Links

A simple C++17 wrapper for HDF5.

Available Modules

module load h5pp/1.9.0-gimpi-2020a
Links

Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content

Available Modules

module load haplocheck/1.3.3
Links

HarfBuzz is an OpenType text shaping engine.

Available Modules

module load HarfBuzz/4.4.1-GCC-11.3.0
Links

HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.

Available Modules

module load HDF/4.2.15-GCCcore-9.2.0
Links

HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.

Available Modules

module load HDF5/1.12.2-iimpi-2022a
Links

help2man produces simple manual pages from the '--help' and '--version' output of other commands.

Available Modules

module load help2man/1.47.8-GCCcore-7.4.0

Warning

Warning: help2man/1.47.8-GCCcore-7.4.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.

Available Modules

module load hifiasm/0.19.7-GCC-11.3.0
Links

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).

Available Modules

module load HISAT2/2.2.1-gimkl-2020a
Links

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

Available Modules

module load HMMER/3.3.2-GCC-9.2.0
Links

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

Available Modules

module load HMMER2/2.3.2-GCC-9.2.0
Links

Available Modules

module load hooks/post-update
Links

Pipeline which focuses on screening MALT data for the presence of a user-specified list of target species.

Available Modules

module load HOPS/0.33

Warning

Warning: HOPS/0.33 is old and marked for deletion. If you still need it, then please let us know.

Links

HPC GridRunner is a simple command-line interface to high throughput computing using a variety of different grid computing platforms, including LSF, SGE, SLURM, and PBS.

Available Modules

module load HpcGridRunner/20181005
Links

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

Available Modules

module load HTSeq/0.13.5-gimkl-2020a-Python-3.9.5
Links

A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix

Available Modules

module load HTSlib/1.12-GCCcore-9.2.0
Links

Pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data.

Available Modules

module load Humann/3.0.0.alpha.3
Links

Spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding.

Available Modules

module load hunspell/1.7.0

Warning

Warning: hunspell/1.7.0 is old and marked for deletion. If you still need it, then please let us know.

Links

The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.

Available Modules

module load hwloc/1.11.13
Links

Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment.

Available Modules

module load HybPiper/2.0.1rc-Miniconda3
Links

Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.

Available Modules

module load hypothesis/6.68.2-gimkl-2022a-Python-3.10.5

Warning

Warning: hypothesis/6.68.2-gimkl-2022a-Python-3.10.5 is old and marked for deletion. If you still need it, then please let us know.

Links

Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.

Available Modules

module load Hypre/2.21.0-gimkl-2022a
Links

Intel C and C++ compilers

Available Modules

module load icc/2018.1.163-GCC-7.4.0
Links

Intel C, C++ & Fortran compilers

Available Modules

module load iccifort/2020.0.166
Links

C/C++ and Java libraries providing Unicode and Globalization support for software applications.

Available Modules

module load ICU/50.2-GCCcore-9.2.0
Links

IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.

Available Modules

module load IDBA-UD/1.1.3-GCC-11.3.0
Links

Intel Fortran compiler

Available Modules

module load ifort/2018.1.163-GCC-7.4.0
Links

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data

Available Modules

module load IGV/2.5.0
Links

Intel C/C++ and Fortran compilers, alongside Intel MPI.

Available Modules

module load iimpi/2018b

Warning

Links

Create, edit, compose, or convert bitmap images

Available Modules

module load ImageMagick/7.0.9-5-GCCcore-9.2.0
Links

Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.

Available Modules

module load imkl/2018.1.163-iimpi-2018b
Links

FFTW interfaces using Intel oneAPI Math Kernel Library

Available Modules

module load imkl-FFTW/2022.0.2-iimpi-2022a
Links

A lightweight JIT compiler for flexible data access in simulation applications

Available Modules

module load impalajit/20211029-foss-2023a
Links

The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. - Homepage: http://software.intel.com/en-us/intel-mpi-library/

Available Modules

module load impi/2017.6.256-iccifort-2017.6.256-GCC-5.4.0
Links

Genotype imputation and haplotype phasing.

Available Modules

module load IMPUTE/2.3.2
Links

Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases for RNA structure and sequence similarities.

Available Modules

module load Infernal/1.1.4-GCC-11.3.0
Links

Available Modules

module load info/exclude
Links

Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications

Available Modules

module load Inspector/2019_update5
Links

Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.

Available Modules

module load intel/2018b
Links

Intel C, C++ & Fortran compilers (classic and oneAPI)

Available Modules

module load intel-compilers/2022.0.2
Links

Sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource.

Available Modules

module load InterProScan/5.62-94.0-gimkl-2022aPerl-5.34.1-Python-3.11.3
Links

Intel based compiler toolchain, including OpenMPI for MPI support, FlexiBLAS (Defaulting to OpenBLAS), FFTW and ScaLAPACK.

Available Modules

module load iofbf/2023a
Links

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.

Available Modules

module load iompi/2023a
Links

ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.

Available Modules

module load ipyrad/0.9.81-Miniconda3

Warning

Links

Efficient phylogenomic software by maximum likelihood

Available Modules

module load IQ-TREE/2.2.0.5-gimpi-2022a
Links

Available Modules

module load IQmol/2.11
Links
Licence

IQmol is proprietary software.

R packages for providing R kernel for Jupyter.

Available Modules

module load IRkernel/1.0.1-gimkl-2018b
Links

Intelligent Storage Acceleration Library

Available Modules

module load ISA-L/2.30.0
Links

Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware.

Available Modules

module load ispc/1.10.0

Warning

Warning: ispc/1.9.2-GCC-5.4.0 is very old and will soon be deleted. If you still need it, then please let us know.

Links

Just Another Gibbs Sampler - a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.

Available Modules

module load JAGS/4.3.1-gimkl-2022a-mt
Links

The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.

Available Modules

module load JasPer/2.0.14-GCCcore-7.4.0
Links

Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.

Available Modules

module load Java/17
Links

JBIG-KIT is a software implementation of the JBIG1 data compression standard

Available Modules

module load jbigkit/2.1-GCCcore-9.2.0
Links

Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Available Modules

module load jcvi/1.0.6-gimkl-2020a-Python-3.8.2
Links

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

Available Modules

module load Jellyfish/2.2.10-gimkl-2020a

Warning

Links

jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.

Available Modules

module load jemalloc/5.2.0-gimkl-2018b
Links

Lightweight and flexible command-line JSON processor.

Available Modules

module load jq/1.5
Links

JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.

Available Modules

module load json-c/0.15-GCCcore-9.2.0
Links

JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.

Available Modules

module load JsonCpp/1.9.3-GCCcore-9.2.0
Links

Available Modules

module load Julia/1.1.0

Warning

Links

A programmer-oriented testing framework for Java.

Available Modules

module load JUnit/4.12-Java-1.8.0_144

Warning

Warning: JUnit/4.12-Java-1.8.0_144 is old and marked for deletion. If you still need it, then please let us know.

Links

An extensible environment for interactive and reproducible computing, based on the Jupyter Notebook and Architecture.

Available Modules

module load JupyterLab/2022.7.0-gimkl-2020a-3.4.3
Links

Java utilities for Bioinformatics

Available Modules

module load jvarkit/2021.10.13-Java-17
Links

Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments

Available Modules

module load Kaiju/1.8.2-gimkl-2020a-Python-3.9.9-Perl-5.30.1-mt
Links

Kalign is a fast multiple sequence alignment program for biological sequences.

Available Modules

module load kalign2/3.3.1-GCCcore-9.2.0
Links

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

Available Modules

module load kallisto/0.46.2-gimkl-2020a
Links

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

Available Modules

module load KAT/2.4.2-gimkl-2018b-Python-3.7.3
Links

KEALib provides an implementation of the GDAL data model. The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software.

Available Modules

module load KEALib/1.4.15-gimpi-2022a
Links

Collection of tools used by the UCSC genome browser.

Available Modules

module load Kent_tools/20200519-linux.x86_64
Links

A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters

Available Modules

module load kineto/0.4.0-GCC-11.3.0
Links

KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.

Available Modules

module load kma/1.4.5-GCC-11.3.0
Links

Disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.

Available Modules

module load KMC/3.1.2rc1-gimkl-2020a-Python-3.8.2
Links

KmerGenie estimates the best k-mer length for genome de novo assembly.

Available Modules

module load KmerGenie/1.7051-gimkl-2022a
Links

Semi-HMM-based Nucleic Acid Parser

Available Modules

module load KorfSNAP/2013-11-29-GCC-9.2.0
Links

Taxonomic sequence classifier.

Available Modules

module load Kraken2/2.0.7-beta-gimkl-2017a.lua
Links

Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

Available Modules

module load KronaTools/2.8.1-GCC-11.3.0-Perl-5.34.1
Links

Library of routines for managing a database.

Available Modules

module load KyotoCabinet/1.2.77-GCCcore-7.4.0

Warning

Warning: KyotoCabinet/1.2.77-GCCcore-7.4.0 is old and marked for deletion. If you still need it, then please let us know.

Links

LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.

Available Modules

module load LAME/3.100-GCCcore-7.4.0
Links

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

Available Modules

module load LAMMPS/23Jun2022-gimkl-2022a-kokkos
Links

LAST finds similar regions between sequences.

Available Modules

module load LAST/1060-gimkl-2020a

Warning

Warning: LAST/1060-gimkl-2020a is old and marked for deletion. If you still need it, then please let us know.

Links

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

Available Modules

module load LASTZ/1.04.22-GCC-12.3.0
Links

D programming language compiler

Available Modules

module load LDC/1.26.0

Warning

Warning: LDC/1.26.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Determines the features most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance

Available Modules

module load LEfSe/1.1.2-gimkl-2022a-R-4.2.1-Python-3.10.5
Links

Available Modules

module load LegacySystemLibs/7
Links

Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples)

Available Modules

module load libaec/1.0.6
Links

Multi-format archive and compression library

Available Modules

module load libarchive/3.7.2-GCC-12.3.0
Links

API for distributing embarrassingly parallel workloads using self-stabilization.

Available Modules

module load libcircle/0.3-iimpi-2020a
Links

Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.

Available Modules

module load libdeflate/1.10
Links

Direct Rendering Manager runtime library.

Available Modules

module load libdrm/2.4.99-GCCcore-9.2.0
Links

The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers

Available Modules

module load libdwarf/20201201-GCCcore-9.2.0
Links

Library for handling OpenGL function pointer management

Available Modules

module load libepoxy/1.5.4-GCCcore-9.2.0
Links

The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.

Available Modules

module load libevent/2.1.8
Links

The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.

Available Modules

module load libffi/3.2.1-gimkl-2017a
Links

libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK.

Available Modules

module load libFLAME/4.0-GCC-11.3.0-amd
Links

Libgpg-error is a small library that defines common error values for all GnuPG components.

Available Modules

module load libgcrypt/1.9.2-GCCcore-9.2.0
Links

GD is an open source code library for the dynamic creation of images by programmers.

Available Modules

module load libgd/2.3.3-GCCcore-12.3.0
Links

Library for reading and writing coordinate system information from/to GeoTIFF files

Available Modules

module load libgeotiff/1.7.1-GCCcore-11.3.0
Links

libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.

Available Modules

module load libgit2/1.6.4-GCC-11.3.0
Links

The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.

Available Modules

module load libGLU/9.0.0-GCCcore-7.4.0
Links

libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.

Available Modules

module load libglvnd/1.2.0

Warning

Links

Libgpg-error is a small library that defines common error values for all GnuPG components.

Available Modules

module load libgpg-error/1.41-GCCcore-9.2.0
Links

Arrays on GPU device memory, for Theano

Available Modules

module load libgpuarray/0.7.6-GCCcore-9.2.0-CUDA-8.0.61
Links

ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream

Available Modules

module load libgtextutils/0.7-gimkl-2017a

Warning

Warning: libgtextutils/0.7-gimkl-2017a is very old and will soon be removed. Please select a more recent version such as libgtextutils/0.7-GCC-11.3.0.

Links

Libiconv converts from one character encoding to another through Unicode conversion

Available Modules

module load libiconv/1.17-GCC-12.3.0
Links

Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.

Available Modules

module load Libint/2.6.0-iimpi-2020a-lmax-6-cp2k

Warning

Links

libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.

Available Modules

module load libjpeg-turbo/2.1.5.1-GCCcore-12.3.0
Links

Reference implementation of OGC KML 2.2

Available Modules

module load libKML/1.3.0.2017-GCC-12.3.0
Links

Generic PCI access library.

Available Modules

module load libpciaccess/0.16-GCCcore-11.3.0
Links

Available Modules

module load libpmi/1
Links

libpng is the official PNG reference library

Available Modules

module load libpng/1.2.58
Links

The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

Available Modules

module load libreadline/6.3-gimkl-2017a
Links

The libsigc++ package implements a typesafe callback system for standard C++.

Available Modules

module load libsigc++/2.10.2-GCCcore-7.4.0.lua
Links

SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.

Available Modules

module load libspatialite/4.3.0a-GCCcore-9.2.0
Links

Set of classes for creating statistical genetic programs.

Available Modules

module load libStatGen/1.0.15-GCC-11.3.0
Links

tiff: Library and tools for reading and writing TIFF data files

Available Modules

module load LibTIFF/4.4.0-GCCcore-11.3.0
Links

GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

Available Modules

module load libtool/2.4.6
Links

This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.

Available Modules

module load libunistring/0.9.6-GCC-5.4.0
Links

Define a portable and efficient C programming API to determine the call-chain of a program.

Available Modules

module load libunwind/1.5.0-GCCcore-9.2.0
Links

libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.

Available Modules

module load libvdwxc/0.4.0-foss-2023a
Links

Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.

Available Modules

module load libxc/6.2.2-intel-2022a
Links

libxml++ is a C++ wrapper for the libxml XML parser library.

Available Modules

module load libxml++/2.40.1-GCCcore-9.2.0.lua
Links

Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).

Available Modules

module load libxml2/2.9.4-gimkl-2017a
Links

Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).

Available Modules

module load libxslt/1.1.29-gimkl-2018b
Links

LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).

Available Modules

module load libxsmm/1.17-GCC-12.3.0
Links

Fast lossless compression algorithm.

Available Modules

module load libzstd/1.5.2-GCC-11.3.0
Links

Tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.

Available Modules

module load Liftoff/1.6.3.2-gimkl-2022a-Python-3.11.3
Links

A web server.

Available Modules

module load lighttpd/1.4.59
Links

Command line tools for Linux to support programmers in developing high performance multi threaded programs.

Available Modules

module load likwid/5.1.0-GCCcore-9.2.0

Warning

Links

Alignment-free scaffolding of genome assembly drafts with long reads

Available Modules

module load LINKS/1.8.5-gimkl-2018b
Links

Color management engine.

Available Modules

module load LittleCMS/2.9-GCCcore-9.2.0
Links

The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.

Available Modules

module load LLVM/14.0.6-GCC-11.3.0-static
Links

LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.

Available Modules

module load LMDB/0.9.29-GCC-11.3.0
Links

Available Modules

module load logs/HEAD
Links

A genome assembly correction and scaffolding pipeline using long reads

Available Modules

module load LongStitch/1.0.4-Miniconda3
Links

Mixed Integer Linear Programming (MILP) solver.

Available Modules

module load lp_solve/5.5.2.5-gimkl-2020a
Links

Least-squares methods to estimate rates and dates from phylogenies

Available Modules

module load LSD2/2.3-GCC-11.3.0
Links

Highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

Available Modules

module load LTR_retriever/2.9.0-gimkl-2020a
Links

A probabilistic framework for structural variant discovery.

Available Modules

module load LUMPY/0.3.1-gimkl-2020a-Python-3.8.2
Links

The light-weight group library defines data structures and collective operations to group MPI processes as an ordered set.

Available Modules

module load lwgrp/1.0.4-iimpi-2020a
Links

LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.

Available Modules

module load lz4/1.9.3-GCCcore-11.3.0
Links

Portable lossless data compression library

Available Modules

module load LZO/2.10-GCCcore-9.2.0
Links

GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.

Available Modules

module load M4/1.4.18-GCCcore-7.4.0
Links

Collection of utilities to manipulate multiple alignments in the Multiple Alignment Format

Available Modules

module load maf_stream/202005-GCC-12.3.0
Links

Multiple sequence alignment program offering a range of methods.

Available Modules

module load MAFFT/7.505-gimkl-2022a-with-extensions
Links

Tool for gene analysis and generalized gene-set analysis of GWAS data.

Available Modules

module load MAGMA/1.08-GCCcore-9.2.0

Warning

Warning: MAGMA/1.08-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.

Available Modules

module load magma/2.5.4-gimkl-2020a-CUDA-11.1.1

Warning

Links

Magma is a large, well-supported software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics. It provides a mathematically rigorous environment for defining and working with structures such as groups, rings, fields, modules, algebras, schemes, curves, graphs, designs, codes and many others. Magma also supports a number of databases designed to aid computational research in those areas of mathematics which are algebraic in nature. whatis([==[Homepage: http://magma.maths.usyd.edu.au/magma/

Available Modules

module load Magma/Magma-2.26.9

Warning

Warning: Magma/Magma-2.26.9 is old and marked for deletion. If you still need it, then please let us know.

Links

Genome annotation pipeline

Available Modules

module load MAKER/2.31.9-gimkl-2018b

Warning

Links

Mamba is a fast, robust, and cross-platform package manager.

Available Modules

module load Mamba/23.1.0-1
Links

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.

Available Modules

module load manta/1.6.0-gimkl-2020a-Python-2.7.18
Links

tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

Available Modules

module load mapDamage/2.2.1
Links

Workflow for effective discovery of SCN loci in flowering plants angiosperms

Available Modules

module load MarkerMiner/1.0-gimkl-2020a-Python-2.7.18
Links

Fast genome and metagenome distance estimation using MinHash

Available Modules

module load Mash/2.3-GCC-11.3.0
Links

Implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences

Available Modules

module load MashMap/3.0.4-Miniconda3
Links

Create a tree using Mash distances.

Available Modules

module load Mashtree/1.4.6-GCC-12.3.0
Links

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).

Available Modules

module load MaSuRCA/4.0.5-gimkl-2020a
Links

matio is an C library for reading and writing Matlab MAT files.

Available Modules

module load MATIO/1.5.17-GCCcore-7.4.0
Links

A high-level language and interactive environment for numerical computing.

Available Modules

module load MATLAB/2021b
Links
Licence

MATLAB is proprietary software.

Access to a valid licence token is required to run MATLAB.

Institution Uptime
University of Waikato 98%
National Institute of Water and Atmospheric Research 0%
Institute of Geological and Nuclear Sciences 99%
Massey University 13%
University of Auckland 98%
University of Otago 100%
Victoria University of Wellington 100%
Auckland University of Technology 12%
University of Canterbury 12%
Plant & Food Research 13%

Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.

Available Modules

module load Maven/3.6.0
Links

MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

Available Modules

module load MaxBin/2.2.7-GCC-11.3.0-Perl-5.34.1
Links

The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.

Available Modules

module load MCL/14.137-gimkl-2018b
Links

The Matlab Compiler Runtime is required for running compiled MATLAB executables without MATLAB itself.

Available Modules

module load MCR/2019a

Warning

Links

Medaka is a tool to create a consensus sequence from nanopore sequencing data.

Available Modules

module load medaka/1.8.0-Miniconda3-22.11.1-1
Links

An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Available Modules

module load MEGAHIT/1.1.4-gimkl-2018b-Python-2.7.16
Links

Tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transcriptome.

Available Modules

module load megalodon/2.5.0-gimkl-2022a-Python-3.10.5
Links

High performance toolkit for complete analysis of methylated RNA data.

Available Modules

module load meRanTK/1.1.1b

Warning

Warning: meRanTK/1.1.1b is old and marked for deletion. If you still need it, then please let us know.

Links

Evaluate genome assemblies with k-mers and more

Available Modules

module load Merqury/1.3-Miniconda3
Links

Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Note that this build enables CPU-based rendering with OpenSWR and LLVM. The module is intended to be used with visualisation software, such as ParaView, on nodes where no GPU hardware is available. Both on-screen and off-screen rendering are supported.

Available Modules

module load Mesa/19.2.1-GCCcore-9.2.0
Links

Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.

Available Modules

module load Meson/0.53.2

Warning

Links

An efficient tool for accurately reconstructing single genomes from complex microbial communities

Available Modules

module load MetaBAT/2.17-GCC-12.3.0
Links

Metabolic And Biogeochemistry anaLyses In microbes

Available Modules

module load METABOLIC/4.0-Miniconda3
Links

MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.

Available Modules

module load MetaEuk/6-GCC-11.3.0
Links

MetaGeneAnnotator is a gene-finding program for prokaryote and phage.

Available Modules

module load MetaGeneAnnotator/20080819-x86-64
Links

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

Available Modules

module load MetaPhlAn/4.0.4-gimkl-2022a-Python-3.10.5
Links

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

Available Modules

module load MetaPhlAn2/2.7.8-gimkl-2018b-Python-3.7.3
Links

Available Modules

module load Metashape/1.6

Warning

Warning: Metashape/1.6 is old and marked for deletion. If you still need it, then please let us know.

Links

Structural-variant caller

Available Modules

module load MetaSV/0.5.4-gimkl-2018b-Python-2.7.16
Links

Flexible pipeline for genome-resolved metagenomic data analysis.

Available Modules

module load metaWRAP/1.2.1-Miniconda3
Links

Taxonomic classification of rRNA.

Available Modules

module load Metaxa2/2.2.2-gimkl-2020a
Links

METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.

Available Modules

module load METIS/5.1.0-GCCcore-9.2.0
Links

mimalloc is a general purpose allocator with excellent performance characteristics.

Available Modules

module load mimalloc/2.0.6-GCC-11.3.0

Warning

Warning: mimalloc/2.0.6-GCC-11.3.0 is old and marked for deletion. If you still need it, then please let us know.

Links

MiMiC: A Framework for Multiscale Modeling in Computational Chemistry This package includes mimicpy

Available Modules

module load MiMiC/0.2.0-gimkl-2022a-Python-3.11.3
Links

The MiMiC communication library (MCL) enables communication between external programs coupled through the MiMiC framework.

Available Modules

module load MiMiC-CommLib/2.0.2-gimkl-2022a
Links

Fast OLC-based de novo assembler for noisy long reads.

Available Modules

module load miniasm/0.3-20191007-GCC-11.3.0
Links

faster and more accurate reimplementation of BUSCO.

Available Modules

module load miniBUSCO/0.2.1-gimkl-2022a
Links

A platform for Python-based data analytics

Available Modules

module load Miniconda3/23.10.0-1
Links

Community-led recipes, infrastructure and distributions for conda.

Available Modules

module load Miniforge3/24.3.0-0
Links

Low memory and more computationally efficient implementation of the genotype imputation algorithms.

Available Modules

module load Minimac3/2.0.1
Links

Low memory and more computationally efficient implementation of the genotype imputation algorithms.

Available Modules

module load Minimac4/4.1.2
Links

Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. .

Available Modules

module load minimap2/2.18-GCC-9.2.0
Links

Aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift..

Available Modules

module load miniprot/0.11-GCC-11.3.0
Links

Completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs

Available Modules

module load miRDeep2/0.1.3-gimkl-2020a
Links

Toolkit which aims to automatically filter pair-end raw data, assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome, and mitogenome visualization.

Available Modules

module load MitoZ/2.3-gimkl-2020a-Python-3.8.2
Links

Fast, and flexible C++ machine learning library with bindings to other languages

Available Modules

module load mlpack/3.4.2-gimkl-2020a

Warning

Warning: mlpack/3.4.2-gimkl-2020a is old and marked for deletion. If you still need it, then please let us know.

Links

MMseqs2: ultra fast and sensitive search and clustering suite

Available Modules

module load MMseqs2/15-6f452-gompi-2023a
Links

A program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.

Available Modules

module load modbam2bed/0.9.4-GCC-11.3.0
Links

Novel dot plot visualization tool used to view tandem repeats

Available Modules

module load ModDotPlot/2023-06-gimkl-2022a-Python-3.11.3
Links

Tool for selecting the best-fit model of evolution for DNA and protein alignments.

Available Modules

module load ModelTest-NG/0.1.7-gompi-2022a
Links

MODFLOW is the U.S. Geological Survey modular finite-difference flow model, which is a computer code that solves the groundwater flow equation. The program is used by hydrogeologists to simulate the flow of groundwater through aquifers.

Available Modules

module load MODFLOW/6.2.2-GCC-9.2.0

Warning

Warning: MODFLOW/6.2.2-GCC-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Tool for working with modified bases from Oxford Nanopore

Available Modules

module load modkit/0.2.5-GCC-12.3.0
Links

Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. The basic philosophy is is to be able to treat general electronic structures for molecules consisting of atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states.

Available Modules

module load Molcas/8.0-15.06.18_CentOS_6.6_x86_64

Warning

Warning: Molcas/8.0-15.06.18_CentOS_6.6_x86_64 is old and marked for deletion. If you still need it, then please let us know.

Links

Molpro is a complete system of ab initio programs for molecular electronic structure calculations.

Available Modules

module load Molpro/mpp-2019.2.2.linux_x86_64_openmp
Links

An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.

Available Modules

module load Mono/6.12.0.122
Links

An analysis toolkit for single-cell RNA-seq.

Available Modules

module load Monocle3/1.0.0-gimkl-2020a-R-4.0.1

Warning

Warning: Monocle3/1.0.0-gimkl-2020a-R-4.0.1 is old and marked for deletion. If you still need it, then please let us know.

Links

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Available Modules

module load mosdepth/0.3.4-GCC-11.3.0
Links

Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

Available Modules

module load Mothur/1.41.0-gimkl-2018b-Python-2.7.16
Links

MpCCI is a vendor neutral and application independent interface for co-simulation. MpCCI offers advanced and proven features for multiphysics modelling.

Available Modules

module load mpcci/4.7.1
Links

The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

Available Modules

module load MPFR/4.0.2-GCCcore-9.2.0
Links

MPI-Based File Utilities For Distributed Systems

Available Modules

module load mpifileutils/0.11-gimpi-2020a
Links

MrBayes is a program for the Bayesian estimation of phylogeny.

Available Modules

module load MrBayes/3.2.7-gimpi-2022a
Links

Multiple Sequentially Markovian Coalescent, infers population size and gene flow from multiple genome sequences

Available Modules

module load MSMC/1.1.0-GCC-7.4.0

Warning

Warning: MSMC/1.1.0-GCC-7.4.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

Available Modules

module load MultiQC/1.13-gimkl-2022a-Python-3.10.5
Links

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.

Available Modules

module load MUMmer/4.0.0rc1-GCCcore-11.3.0
Links

A parallel sparse direct solver

Available Modules

module load MUMPS/4.10.0-gimkl-2020a-metis-4.0.3
Links

muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression.

Available Modules

module load muParser/2.2.5-GCC-11.3.0
Links

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two.

Available Modules

module load MUSCLE/3.8.31
Links

MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user.

Available Modules

module load MUST/1.6-gimkl-2020a-Python-3.8.2

Warning

Warning: MUST/1.6-gimkl-2020a-Python-3.8.2 is old and marked for deletion. If you still need it, then please let us know.

Links

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Available Modules

module load NAMD/2.12-gimkl-2017a-cuda
Links

Available Modules

module load nano/3
Links

Comparing runs of Oxford Nanopore sequencing data and alignments

Available Modules

module load NanoComp/1.20.0-gimkl-2022a-Python-3.10.5
Links

Filtering and trimming of long read sequencing data.

Available Modules

module load nanofilt/2.6.0-gimkl-2020a-Python-3.8.2
Links

Functions to extract information from Oxford Nanopore sequencing data and alignments

Available Modules

module load nanoget/1.16.1-gimkl-2020a-Python-3.8.2
Links

Removing reads mapping to the lambda genome.

Available Modules

module load NanoLyse/1.2.0-gimkl-2020a
Links

A few simple math function for other Oxford Nanopore processing scripts

Available Modules

module load nanomath/1.2.1-gimkl-2022a-Python-3.10.5
Links

Plotting suite for Oxford Nanopore sequencing data and alignments.

Available Modules

module load NanoPlot/1.41.0-gimkl-2022a-Python-3.10.5
Links

Software package for signal-level analysis of Oxford Nanopore sequencing data.

Available Modules

module load nanopolish/0.13.3-gimkl-2020a-Python-3.9.9
Links

Create fastQC-like plots for Oxford Nanopore sequencing data.

Available Modules

module load nanoQC/0.9.4-gimkl-2022a-Python-3.10.5
Links

Tool for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.

Available Modules

module load NanoStat/1.5.0-gimkl-2020a-Python-3.8.2
Links

NASM: General-purpose x86 assembler

Available Modules

module load NASM/2.15.05
Links

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

Available Modules

module load ncbi-vdb/2.11.2-gimpi-2022a
Links

The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.

Available Modules

module load NCCL/2.10.3-CUDA-11.4.1
Links

NCL is an interpreted language designed specifically for scientific data analysis and visualization.

Available Modules

module load NCL/6.6.2-foss-2023a
Links

manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5

Available Modules

module load NCO/4.8.1-gimpi-2022a
Links

The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.

Available Modules

module load ncurses/6.0-gimkl-2017a
Links

Visual browser for netCDF format files.

Available Modules

module load ncview/2.1.7-gimkl-2018b
Links

ne is a free (GPL'd) text editor based on the POSIX standard that runs (we hope) on almost any UN*X machine. ne is easy to use for the beginner, but powerful and fully configurable for the wizard, and most sparing in its resource usage.

Available Modules

module load ne/3.0.1
Links

Available Modules

module load nearline/1.1.0
Links

Rrror correction and de-novo assembly tool for Nanopore long noisy reads

Available Modules

module load NECAT/0.0.1-GCC-11.3.0
Links

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Available Modules

module load netCDF/4.6.2-gimpi-2018b
Links

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Available Modules

module load netCDF-C++/4.2-intel-2020a
Links

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Available Modules

module load netCDF-C++4/4.3.1-iimpi-2020a

Warning

Warning: netCDF-C++4/4.3.1-iimpi-2020a is old and marked for deletion. Please select a more recent version (try 'module spider netCDF-C++4') or let us know that you still need it.

Links

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Available Modules

module load netCDF-Fortran/4.6.0-iimpi-2022a
Links

This implements a Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories.

Available Modules

module load NewHybrids/1.1_Beta3-GCC-11.3.0
Links

NX is a general-purpose program package for simulating the dynamics of electronically excited molecules and molecular assemblies.

Available Modules

module load Newton-X/2.4-gimkl-2022a
Links

Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data

Available Modules

module load Nextflow/22.04.3
Links

NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime.

Available Modules

module load NextGenMap/0.5.5-GCC-11.3.0

Warning

Warning: NextGenMap/0.5.5-GCC-11.3.0 is old and marked for deletion. If you still need it, then please let us know.

Links

NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.

Available Modules

module load NGS/1.2.5-gimkl-2017a

Warning

Links

Nim is a systems and applications programming language.

Available Modules

module load Nim/1.6.14-GCC-11.3.0
Links

Ninja is a small build system with a focus on speed.

Available Modules

module load Ninja/1.10.0
Links

NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms

Available Modules

module load NLopt/2.5.0-gimkl-2018b
Links

Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.

Available Modules

module load nodejs/14.16.1-GCCcore-9.2.0
Links

Available Modules

module load NONMEM/7.5
Links

Used to mask nucleic acid sequences

Available Modules

module load nseg/1998-GCC-9.2.0
Links

NVIDIA® Nsight™ Compute is an interactive kernel profiler for CUDA applications. It provides detailed performance metrics and API debugging via a user interface and command line tool.

Available Modules

module load Nsight-Compute/2023.2.2.3
Links

NVIDIA® Nsight™ Systems is a system-wide performance analysis tool designed to visualize an application’s algorithm, help you select the largest opportunities to optimize, and tune to scale efficiently across any quantity of CPUs and GPUs

Available Modules

module load Nsight-Systems/2020.5.1
Links

Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.

Available Modules

module load NSPR/4.25-GCCcore-9.2.0
Links

Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.

Available Modules

module load NSS/3.51-GCCcore-9.2.0
Links

nsync is a C library that exports various synchronization primitives, such as mutexes

Available Modules

module load nsync/1.24.0-GCCcore-9.2.0
Links

Reads to report pipeline for bacterial isolate NGS data.

Available Modules

module load nullarbor/2.0.20191013_LIC
Links

The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.

Available Modules

module load numactl/2.0.14-intel-compilers-2022.0.2
Links

C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)

Available Modules

module load NVHPC/21.9-GCC-11.3.0-CUDA-11.4.1
Links

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.

Available Modules

module load NWChem/6.8.1.revision133-gimkl-2018b-2018-06-14-Python-2.7.16
Links

Manipulate various data and sequence files.

Available Modules

module load OBITools/1.2.13
Links

Available Modules

module load objects/info
Links

Orthologous MAtrix project is a method and database for the inference of orthologs among complete genomes

Available Modules

module load OMA/2.4.1
Links

Data processing toolkit that contains the Oxford Nanopore Technologies' basecalling algorithms, and several bioinformatic post-processing features

Available Modules

module load ont-guppy-gpu/6.4.6
Links

source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.

Available Modules

module load OPARI2/2.0.5-GCCcore-9.2.0
Links

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

Available Modules

module load OpenBabel/2.4.1-GCC-7.4.0
Links

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

Available Modules

module load OpenBLAS/0.3.6-GCC-9.2.0

Warning

Links

OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.

Available Modules

module load OpenCV/3.4.7-gimkl-2020a
Links

Wind turbine multiphysics simulation tool

Available Modules

module load OpenFAST/2.1.0-gimkl-2018b

Warning

Warning: OpenFAST/2.1.0-gimkl-2018b is old and marked for deletion. If you still need it, then please let us know.

Links

OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

Available Modules

module load OpenFOAM/v1812-gimkl-2018b-libAcoustics
Links

An open-source JPEG 2000 codec written in C

Available Modules

module load OpenJPEG/2.5.0-GCCcore-12.3.0
Links

The Open MPI Project is an open source MPI-3 implementation.

Available Modules

module load OpenMPI/4.1.1-GCC-9.2.0
Links

Simulates the performance of structural and geotechnical systems subjected to earthquakes.

Available Modules

module load OpenSees/3.2.0-gimkl-2020a-METIS4
Links

Wraps OpenSees for Python. Load an OpenSees module as well.

Available Modules

module load OpenSeesPy/3.3.0.0
Links

OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).

Available Modules

module load OpenSlide/3.4.1-GCC-11.3.0
Links

The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.

Available Modules

module load OpenSSL/1.1.0e-gimkl-2017a
Links

ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.

Available Modules

module load ORCA/4.0.1-OpenMPI-2.0.2
Links

A simple and not slow open reading frame (ORF) caller.

Available Modules

module load OrfM/0.7.1-GCC-11.3.0

Warning

Warning: OrfM/0.7.1-GCC-11.3.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Identifies missing annotations for evolutionarily conserved genes.

Available Modules

module load OrthoFiller/1.1.4-gimkl-2018b-Python-2.7.16

Warning

Warning: OrthoFiller/1.1.4-gimkl-2018b-Python-2.7.16 is old and marked for deletion. If you still need it, then please let us know.

Links

OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics

Available Modules

module load OrthoFinder/2.5.2-gimkl-2020a-Python-3.8.2
Links

Genome-scale algorithm for grouping orthologous protein sequences.

Available Modules

module load OrthoMCL/2.0.9-gimkl-2020a-Perl-5.30.1

Warning

Warning: OrthoMCL/2.0.9-gimkl-2020a-Perl-5.30.1 is old and marked for deletion. If you still need it, then please let us know.

Links

OSPRay features interactive CPU rendering capabilities geared towards Scientific Visualization applications. Advanced shading effects such as Ambient Occlusion, shadows, and transparency can be rendered interactively, enabling new insights into data exploration.

Available Modules

module load OSPRay/1.8.2-GCCcore-7.4.0
Links

OSU Micro-Benchmarks for MPI

Available Modules

module load OSU-Micro-Benchmarks/6.2-gimpi-2022a
Links

The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library

Available Modules

module load OTF2/2.2-GCCcore-9.2.0
Links

Prokaryotic Antiviral Defence LOCator

Available Modules

module load padloc/2.0.0-foss-2023a-R-4.3.2
Links

CLI tools to process mapped Hi-C data

Available Modules

module load pairtools/1.0.2-gimkl-2022a-Python-3.10.5
Links

pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data.

Available Modules

module load PALEOMIX/1.2.14
Links

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

Available Modules

module load PAML/4.10.7-GCC-12.3.0
Links

A pangenome analysis pipeline.

Available Modules

module load panaroo/1.3.0-gimkl-2022a-Python-3.10.5
Links

Almost universal document converter

Available Modules

module load pandoc/2.8.0.1
Links

Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.

Available Modules

module load Pango/1.47.0-GCCcore-9.2.0
Links

PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.

Available Modules

module load PAPI/6.0.0-GCCcore-9.2.0
Links

Build and execute shell commands in parallel

Available Modules

module load Parallel/20190622
Links

parallel fastq-dump wrapper

Available Modules

module load parallel-fastq-dump/0.6.6-gimkl-2020a-Python-3.8.2

Warning

Links

A high-level Parallel I/O Library for structured grid applications

Available Modules

module load ParallelIO/2.5.4-intel-2020a
Links

parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms.

Available Modules

module load parasail/2.4.3

Warning

Warning: parasail/2.4.3 is old and marked for deletion. If you still need it, then please let us know.

Links

ParaView is a scientific parallel visualizer. This version supports CPU-only rendering without X context using the OSMesa library, it does not support GPU rendering. Use the GALLIUM_DRIVER environment variable to choose a software renderer, it is recommended to use GALLIUM_DRIVER=swr for best performance. Ray tracing using the OSPRay library is also supported.

Available Modules

module load ParaView/5.6.0-gimpi-2018b
Links

ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.

Available Modules

module load ParMETIS/4.0.3-foss-2023a
Links

PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.

Available Modules

module load patchelf/0.14.5-GCC-11.3.0
Links

Tools for plotting Oxford Nanopore and other long-read data.

Available Modules

module load pauvre/0.2.3-gimkl-2020a-Python-3.8.2
Links

The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

Available Modules

module load PCRE/8.43-GCCcore-7.4.0
Links

The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

Available Modules

module load PCRE2/10.42-GCCcore-12.3.0
Links

Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools.

Available Modules

module load PDT/3.25.1-GCCcore-9.2.0
Links

Memory-efficient,fully parallelized and highly accurate pair-end read merger.

Available Modules

module load PEAR/0.9.11-GCCcore-9.2.0
Links

Genome assembler for long reads (length > 10kb, accuracy > 99%). Based on Sparse HIereachical MimiMizER (SHIMMER) for fast read-to-read overlaping

Available Modules

module load Peregrine/0.1.6.1-gimkl-2020a
Links

Larry Wall's Practical Extraction and Report Language

Available Modules

module load Perl/5.28.1-gimkl-2018b
Links

PEST++ is a software suite aimed at supporting complex numerical models in the decision-support context. Much focus has been devoted to supporting environmental models (groundwater, surface water, etc) but these tools are readily applicable to any computer model.

Available Modules

module load PEST++/5.1.5-gimkl-2020a

Warning

Warning: PEST++/5.1.5-gimkl-2020a is old and marked for deletion. If you still need it, then please let us know.

Links

PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

Available Modules

module load PETSc/3.9.3-gimkl-2018b
Links

PanGenome Graph Builder(pggb)

Available Modules

module load pggb/0.5.3-Miniconda3
Links

pangenome graph evaluator

Available Modules

module load pgge/2021-Miniconda3
Links

A tool to visualize phase block structure from (many) BAM or CRAM files together with BED annotation

Available Modules

module load PHASIUS/0.1.0d-GCC-11.3.0
Links

Phonopy is an open source package of phonon calculations based on the supercell approach.

Available Modules

module load phonopy/2.28.0-foss-2023a
Links

Integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.

Available Modules

module load PhyloPhlAn/3.0.1-gimkl-2020a-Python-3.8.2
Links

Phylogenetic estimation using Maximum Likelihood

Available Modules

module load PhyML/3.3.20211231-gimpi-2022a
Links

phyx performs phylogenetics analyses on trees and sequences.

Available Modules

module load phyx/1.3-gimkl-2022a
Links

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

Available Modules

module load picard/2.26.10-Java-11.0.4
Links

parallel implementation of gzip,

Available Modules

module load pigz/2.7
Links

Pilon is an automated genome assembly improvement and variant detection tool

Available Modules

module load Pilon/1.24-Java-15.0.2
Links

Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.

Available Modules

module load pixman/0.40.0
Links

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

Available Modules

module load PLINK/1.09b6.16
Links

PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.

Available Modules

module load PLUMED/2.7.3-intel-2020a

Warning

Links

Parallel netCDF: A Parallel I/O Library for NetCDF File Access

Available Modules

module load PnetCDF/1.13.0-gompi-2023a
Links

File format for storing nanopore dna data in an easily accessible way.

Available Modules

module load pod5/0.2.4-gimkl-2022a
Links

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity

Available Modules

module load Porechop/0.2.4-gimkl-2022a-Python-3.11.3
Links

Extension of Porechop whose purpose is to process adapter sequences in ONT reads

Available Modules

module load Porechop_ABI/0.5.0-foss-2023a
Links

Object-relational database system.

Available Modules

module load PostgreSQL/12.2-GCC-9.2.0
Links

Places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment

Available Modules

module load pplacer/1.1.alpha19
Links

Probabilistic multiple alignment program for DNA, codon and amino-acid sequences. .

Available Modules

module load PRANK/170427-gimkl-2022a
Links

Software for predicting library complexity and genome coverage in high-throughput sequencing.

Available Modules

module load preseq/3.2.0-GCC-11.3.0
Links

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.

Available Modules

module load prodigal/2.6.3-GCC-9.2.0
Links

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.

Available Modules

module load Prodigal/2.6.3-GCC-9.2.0
Links

A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes.

Available Modules

module load prodigal-gv/2.9.0-GCC-11.3.0
Links

Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates

Available Modules

module load PROJ/5.2.0-gimkl-2018b
Links

Prokka is a software tool for the rapid annotation of prokaryotic genomes.

Available Modules

module load prokka/1.13.4-gimkl-2018b.lua
Links

Proteinortho is a tool to detect orthologous genes within different species.

Available Modules

module load Proteinortho/6.0.28-gimkl-2020a-Python-3.8.2-Perl-5.30.1
Links

Pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.

Available Modules

module load ProtHint/2.6.0-gimkl-2022a-Perl-5.34.1-Python-3.11.3
Links

Google Protocol Buffers.

Available Modules

module load protobuf/23.0-GCC-11.3.0
Links

Infers population size history from a diploid sequence using the PSMC model.

Available Modules

module load psmc/0.6.5-gimkl-2018b
Links

Generates inline-Assembly for sparse Matrix Multiplication.

Available Modules

module load PSpaMM/0.2.1-foss-2023a-Python-3.11.6
Links

pstoedit translates PostScript and PDF graphics into other vector formats

Available Modules

module load pstoedit/3.75-GCCcore-9.2.0
Links

Utility program for extracting sequences from a fasta/fastq file

Available Modules

module load pullseq/1.0.2-GCCcore-7.4.0
Links

parallel unstructured mesh infrastructure API

Available Modules

module load PUMI/2.2.7-foss-2023a
Links

purge haplotigs and overlaps in an assembly based on read depth

Available Modules

module load purge_dups/1.2.6-gimkl-2022a-Python-3.10.5
Links

Pipeline to help with curating heterozygous diploid genome assemblies

Available Modules

module load purge_haplotigs/1.1.2-gimkl-2022a-Perl-5.34.1
Links

Monitors the progress of data through a unix pipeline.

Available Modules

module load pv/1.6.6
Links

Whole-genome classification using Average Nucleotide Identity

Available Modules

module load pyani/0.2.10-gimkl-2020a-Python-3.8.2

Warning

Links

Computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.

Available Modules

module load pycoQC/2.5.2-gimkl-2020a-Python-3.8.2
Links

PyMOL (open source version) molecular visualization system.

Available Modules

module load pymol-open-source/2.5.0
Links

PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.

Available Modules

module load PyOpenGL/3.1.5-gimkl-2018b-Python-2.7.16
Links

PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.

Available Modules

module load PyQt/5.12.1-gimkl-2020a-Python-3.8.2
Links

Python bindings to spoa.

Available Modules

module load pyspoa/0.0.8-gimkl-2018b-Python-3.8.1
Links

Python is a programming language that lets you work more quickly and integrate your systems more effectively.

Available Modules

module load Python/3.10.5-gimkl-2022a
Links

GDAL, pyModis, RIOS, Fiona, Shapely, descartes and pygrib - Python packages for geospatial data I/O, mostly based on the OSGEO libraries GDAL and OGR

Available Modules

module load Python-Geo/3.8.2-gimkl-2020
Links

Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.

Available Modules

module load PyTorch/1.12.1-gimkl-2022a-Python-3.10.5-CUDA-11.6.2
Links

Command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files

Available Modules

module load qcat/1.1.0-gimkl-2020a-Python-3.8.2
Links

Available Modules

module load QChem/6.0.2-mpi
Links
Licence

QChem is proprietary software.

An open-source bioinformatics pipeline for microbiome analysis from raw DNA sequencing data.

Available Modules

module load QIIME2/2023.5
Links

Qt is a comprehensive cross-platform C++ application framework.

Available Modules

module load Qt5/5.10.1-GCCcore-7.4.0
Links

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

Available Modules

module load QuantumESPRESSO/7.2-intel-2022a
Links

Evaluates genome assemblies

Available Modules

module load QUAST/5.2.0-foss-2023a
Links

Efficient implementation of the Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments .

Available Modules

module load QuickTree/2.5-GCC-12.3.0
Links

R is a free software environment for statistical computing and graphics.

Available Modules

module load R/4.2.1-gimkl-2022a
Links

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.

Available Modules

module load R-bundle-Bioconductor/3.15-gimkl-2022a-R-4.2.1
Links

R packages for Geometric and Geospatial data which depend on GEOS and/or GDAL.

Available Modules

module load R-Geo/4.2.1-gimkl-2022a
Links

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.

Available Modules

module load Racon/1.4.13-GCC-9.2.0
Links

Tool for chromosome assembly using multiple references.

Available Modules

module load Ragout/2.2-gimkl-2018b-Python-2.7.16
Links

Minimum free energy of folding randomization test software

Available Modules

module load randfold/2.0.1-GCC-9.2.0
Links

Available Modules

module load RANGS-GSHHS/20171003
Links

An algorithmic engineered implementation of canonical neighbour-joining.

Available Modules

module load RapidNJ/2.3.2
Links

Randomly subsample sequencing reads to a specified coverage.

Available Modules

module load rasusa/0.6.1-GCCcore-9.2.0
Links

Phased hybrid error correction of long reads using colored de Bruijn graphs

Available Modules

module load Ratatosk/0.9.0-GCC-12.3.0
Links

De novo genome assembler for long uncorrected reads.

Available Modules

module load Raven/1.4.0-GCC-9.2.0

Warning

Links

RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.

Available Modules

module load RAxML/8.2.10-gimkl-2017a

Warning

Links

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.

Available Modules

module load RAxML-NG/1.1.0-gimkl-2022a
Links

Tool for mapping millions of short genomic reads onto a reference genome.

Available Modules

module load razers3/3.5.8

Warning

Warning: razers3/3.5.8 is old and marked for deletion. If you still need it, then please let us know.

Links

Rclone is a command line program to sync files and directories to and from a variety of online storage services

Available Modules

module load rclone/1.54.0
Links

kmer-based error correction method for RNA-seq data.

Available Modules

module load Rcorrector/1.0.4-gimkl-2020a
Links

rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies. rDock is mainly written in C++ and accessory scripts and programs are written in C++, perl or python languages.

Available Modules

module load rDock/2013.1-gimkl-2018b

Warning

Warning: rDock/2013.1-gimkl-2018b is old and marked for deletion. If you still need it, then please let us know.

Links

The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.

Available Modules

module load RDP-Classifier/2.12
Links

fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++library.

Available Modules

module load RE2/2023-08-01-GCC-11.3.0
Links

re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons.

Available Modules

module load re2c/1.3
Links

De novo identification and classification of repeat sequence families from genomic sequences

Available Modules

module load RECON/1.08-GCC-9.2.0
Links

Available Modules

module load refs/remotes
Links

RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).

Available Modules

module load Relion/2.1-gimkl-2017a.lua
Links

Screens DNA sequences for interspersed repeats and low complexity DNA sequences. For licensing reasons RepBase is not included, instead you must set LIBDIR to point at a directory which contains your copy of it.

Available Modules

module load RepeatMasker/4.1.0-gimkl-2018b
Links

De novo transposable element (TE) family identification and modeling package.

Available Modules

module load RepeatModeler/2.0.2a-gimkl-2020a
Links

De novo identification of repeat families in large genomes

Available Modules

module load RepeatScout/1.0.5-GCC-9.2.0-Perl-5.30.1-mt
Links

Tool for visualizing alignments of reads in regions containing tandem repeats

Available Modules

module load REViewer/0.2.7
Links

Structure generation, with or without conditional information (a motif, target etc) It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper.

Available Modules

module load RFdiffusion/1.1.0-gimkl-2022a-Python-3.10.5
Links

Predicting plasmid contigs from assemblies

Available Modules

module load RFPlasmid/0.0.18-gimkl-2022a-Python-3.10.5
Links

RiskScape is an open-source spatial data processing application used for multi-hazard risk analysis. RiskScape is highly customisable, letting modellers tailor the risk analysis to suit the problem domain and input data being modelled.

Available Modules

module load Riskscape/1.2.0
Links

A common set of C++ infrastructure and CMake utilities used by various components of Intel® oneAPI Rendering Toolkit.

Available Modules

module load rkcommon/1.6.0-GCCcore-9.2.0

Warning

Warning: rkcommon/1.6.0-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include: Support for custom matrices ( without KA-Statistics ). Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm. Support for cross_match-like masklevel filtering..

Available Modules

module load RMBlast/2.10.0-GCC-9.2.0
Links

consistent and rapid annotation of ribosomal RNA genes.

Available Modules

module load RNAmmer/1.2-GCC-9.2.0-Perl-5.30.1
Links

Tool for evaluating RNA-Seq assemblies using reference genome and gene database

Available Modules

module load rnaQUAST/2.2.2-gimkl-2022a
Links

Rapid large-scale prokaryote pan genome analysis

Available Modules

module load Roary/3.13.0-gimkl-2020a
Links

Platform for GPU Enabled HPC and UltraScale Computing

Available Modules

module load ROCm/4.2.0-GCC-9.2.0-amd

Warning

Warning: ROCm/4.2.0-GCC-9.2.0-amd is old and marked for deletion. If you still need it, then please let us know.

Links

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.

Available Modules

module load ROOT/6.16.00-GCC-7.4.0
Links

Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids.

Available Modules

module load Rosetta/3.13-gimkl-2022a
Links

Estimates gene and isoform expression levels from RNA-Seq data

Available Modules

module load RSEM/1.3.3-gimkl-2022a
Links

The Remote Sensing and GIS software library (RSGISLib) is a collection of tools for processing remote sensing and GIS datasets. The tools are accessed using Python bindings or an XML interface.

Available Modules

module load RSGISLib/5.0.10-gimkl-2022a-Python-3.10.5
Links

RStudio-Server for OpenOnDemand.

Available Modules

module load RStudio-Server/2024.04.2-764
Links

Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.

Available Modules

module load Ruby/3.0.1-GCC-11.3.0
Links

Systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.

Available Modules

module load Rust/1.80.1-GCC-12.3.0
Links

FM-index Long Read Corrector (Rust implementation)

Available Modules

module load rust-fmlrc/0.1.7-GCC-11.3.0

Warning

Warning: rust-fmlrc/0.1.7-GCC-11.3.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Ppackage containing programs for use in the genetic analysis of family, pedigree and individual data.

Available Modules

module load SAGE/6.4
Links

Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.

Available Modules

module load Salmon/1.4.0-gimkl-2020a
Links

Tools for working with SAM/BAM data

Available Modules

module load Sambamba/0.7.1

Warning

Links

samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.

Available Modules

module load samblaster/0.1.26-GCC-9.2.0
Links

Filter SAM file for soft and hard clipped alignments.

Available Modules

module load samclip/0.4.0-GCC-11.3.0
Links

Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format

Available Modules

module load SAMtools/0.1.18-gimkl-2018b
Links

SAS is a statistical software suite developed by SAS Institute for data management, advanced analytics, multivariate analysis, business intelligence, criminal investigation, and predictive analytics. - Homepage: https://www.sas.com/en_nz/home.html/

Available Modules

module load SAS/9.4
Links

Interface to various variant calling formats.

Available Modules

module load savvy/2.1.0-GCC-11.3.0
Links

sbt is a build tool for Scala, Java, and more.

Available Modules

module load sbt/1.7.2-Java-1.8.0_144

Warning

Warning: sbt/1.7.2-Java-1.8.0_144 is old and marked for deletion. If you still need it, then please let us know.

Links

Bioconductor bundle for single-cell RNA-Seq Data analysis

Available Modules

module load sc-RNA/2023-07-gimkl-2022a-R-bundle-Bioconductor-3.15-R-4.2.1
Links

The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.

Available Modules

module load ScaLAPACK/2.2.0-gompi-2023a-fb
Links

SCons is a software construction tool.

Available Modules

module load SCons/3.0.1
Links

Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.

Available Modules

module load SCOTCH/6.1.2-gimpi-2022a
Links

Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies.

Available Modules

module load screen_assembly/1.2.8-gimkl-2022a-Python-3.11.3
Links

Simple DirectMedia Layer, a cross-platform multimedia library

Available Modules

module load SDL2/2.0.9-GCCcore-9.2.0
Links

SeisSol is a software package for simulating wave propagation and dynamic rupture based on the arbitrary high-order accurate derivative discontinuous Galerkin method (ADER-DG).

Available Modules

module load SeisSol/1.1.4-foss-2023a-Python-3.11.6
Links

SATe-enabled Phylogenetic Placement. Phylogenetic placement of short reads into reference alignments and trees.

Available Modules

module load SEPP/4.5.1-gimkl-2022a-Python-3.11.3
Links

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.

Available Modules

module load SeqAn/2.4.0-GCCcore-9.2.0

Warning

Warning: SeqAn/2.4.0-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.

Available Modules

module load SeqAn3/3.0.0

Warning

Links

Ultrafast toolkit for FASTA/Q file manipulation

Available Modules

module load SeqKit/2.1.0
Links

Seqmagick is a utility built in the spirit of imagemagick to expose the file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.

Available Modules

module load seqmagick/0.7.0-gimkl-2018b-Python-3.7.3
Links

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.

Available Modules

module load seqtk/1.3-gimkl-2018b
Links

Estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data.

Available Modules

module load SHAPEIT4/4.2.0-GCC-9.2.0
Links

A std::streambuf wrapper for compression formats.

Available Modules

module load shrinkwrap/1.2.0-GCC-11.3.0
Links

A comparative genomics tool for analysing genomic variations that correlate with pathogens, or microorganisms adapt in different environments.

Available Modules

module load SiBELia/3.0.7
Links

SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

Available Modules

module load Siesta/4.1-b4-intel-2020a
Links

SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms

Available Modules

module load SignalP/5.0b
Links

A general-purpose genome simulator

Available Modules

module load simuG/1.0.1-GCC-11.3.0
Links

Singularity is a portable application stack packaging and runtime utility.

Available Modules

module load Singularity/3.11.3

Warning

Warning: Singularity is deprecated at NeSI, please switch to using Apptainer instead.

Links

Scalable I/O library for parallel access to task-local files.

Available Modules

module load SIONlib/1.7.7-GCC-11.3.0

Warning

Warning: SIONlib/1.7.7-GCC-11.3.0 is old and marked for deletion. Please select a more recent version (try 'module spider SIONlib') or let us know that you still need it.

Links

SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.

Available Modules

module load SIP/4.19.8-gimkl-2020a-Python-3.8.2

Warning

Warning: SIP/4.19.8-gimkl-2020a-Python-3.8.2 is old and marked for deletion. Please select a more recent version (try 'module spider SIP') or let us know that you still need it.

Links

Simulation of In Silico Multi-Omic Networks R package.

Available Modules

module load sismonr/2.0.0-gimkl-2020a-R-4.1.0

Warning

Warning: sismonr/2.0.0-gimkl-2020a-R-4.1.0-Julia-1.7.1 is old and marked for deletion. If you still need it, then please let us know.

Links

accurate, fast nucleotide identity calculation for MAGs, genomes, and databases

Available Modules

module load skani/0.2.2-GCC-12.3.0
Links

SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs.

Available Modules

module load SKESA/2.4.0-gimpi-2022a_saute.1.3.0_1
Links

Toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.

Available Modules

module load slow5tools/0.8.0-gimpi-2022a
Links

Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length.

Available Modules

module load smafa/0.5.0-GCC-11.3.0
Links

simplifies and speeds calling and genotyping SVs for short reads.

Available Modules

module load smoove/0.2.8-Miniconda3
Links

PacBio’s open-source software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.

Available Modules

module load SMRT-Link/8.0.0.80529-cli-tools-only
Links

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.

Available Modules

module load snakemake/7.32.3-gimkl-2022a-Python-3.11.3
Links

SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping proposed by Chen and Zebker

Available Modules

module load snaphu/2.0.4-GCCcore-9.2.0

Warning

Warning: snaphu/2.0.4-GCCcore-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.

Available Modules

module load snappy/1.1.7-GCCcore-7.4.0
Links

A fast structural variant caller for long-read sequencing.

Available Modules

module load Sniffles/2.0.7-gimkl-2022a-Python-3.10.5
Links

Finds SNP sites from a multi-FASTA alignment file.

Available Modules

module load snp-sites/2.5.1-GCC-11.3.0
Links

SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).

Available Modules

module load snpEff/5.0-Java-11.0.4
Links

SNVoter - A top up tool to enhance SNV calling from Nanopore sequencing data & NanoMethPhase - Phase long reads and CpG methylations from Oxford Nanopore Technologies.

Available Modules

module load SNVoter-NanoMethPhase/1.0
Links

Database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++.

Available Modules

module load SOCI/4.0.2-GCC-9.2.0

Warning

Warning: SOCI/4.0.2-GCC-9.2.0 is old and marked for deletion. If you still need it, then please let us know.

Links

extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF

Available Modules

module load somalier/0.2.16
Links

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.

Available Modules

module load SortMeRNA/2.1-gimkl-2017a

Warning

Links

SourceTracker is a Bayesian approach to estimating the proportion of a novel community that comes from a set of source environments.

Available Modules

module load SourceTracker/0.9.6
Links

Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.

Available Modules

module load Spack/0.17.0
Links

Genome assembler for single-cell and isolates data sets

Available Modules

module load SPAdes/3.15.2-gimkl-2020a
Links

Stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.

Available Modules

module load spaln/2.4.13f-GCC-11.3.0
Links

Spark is Hadoop MapReduce done in memory

Available Modules

module load Spark/2.3.1-gimkl-2018b-Hadoop-2.7
Links

Fast C++ logging library.

Available Modules

module load spdlog/1.10.0-GCCcore-11.3.0
Links

C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.

Available Modules

module load SpectrA/1.0.1-GCCcore-12.3.0
Links

System for Processing Image Data from Electron microscopy and Related fields

Available Modules

module load SPIDER/22.02

Warning

Warning: SPIDER/22.02 is old and marked for deletion. If you still need it, then please let us know.

Links

Available Modules

module load splat/1.0
Links

c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences

Available Modules

module load spoa/4.0.7-GCC-9.2.0
Links

SQLite: SQL Database Engine in a C Library

Available Modules

module load SQLite/3.31.1-GCCcore-9.2.0
Links

fully automated metagenomics pipeline, from reads to bins.

Available Modules

module load SqueezeMeta/1.6.0-Miniconda3
Links

The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format

Available Modules

module load sratoolkit/2.9.6

Warning

Links

Available Modules

module load srun-wrapper/1
Links

Pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.

Available Modules

module load SSAHA2/2.5.5-x86_64
Links

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

Available Modules

module load Stacks/2.41-gimkl-2018b

Warning

Links

Fast universal RNA-seq aligner

Available Modules

module load STAR/2.7.9a-GCC-9.2.0
Links

Processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set

Available Modules

module load STAR-Fusion/1.6.0-gimkl-2018b

Warning

Warning: STAR-Fusion/1.6.0-gimkl-2018b is old and marked for deletion. If you still need it, then please let us know.

Links

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

Available Modules

module load StringTie/2.2.0-gimkl-2022a
Links

The program structure is a free software package for using multi-locus genotype data to investigate population structure.

Available Modules

module load Structure/2.3.4-iccifort-2020.0.166
Links

Available Modules

module load sublime/3
Links

High performance read alignment, quantification and mutation discovery

Available Modules

module load Subread/2.0.3-GCC-11.3.0
Links

Subversion is an open source version control system. Subversion exists to be universally recognized and adopted as an open-source, centralized version control system characterized by its reliability as a safe haven for valuable data; the simplicity of its model and usage; and its ability to support the needs of a wide variety of users and projects, from individuals to large-scale enterprise operations.

Available Modules

module load Subversion/1.9.7
Links

SuiteSparse is a collection of libraries manipulate sparse matrices.

Available Modules

module load SuiteSparse/5.13.0-gimkl-2022a
Links

SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers

Available Modules

module load SUNDIALS/4.1.0-gimkl-2018b

Warning

Links

Solution of large, sparse, nonsymmetric systems of linear equations.

Available Modules

module load SuperLU/5.2.1-gimkl-2020a
Links

Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source

Available Modules

module load Supernova/2.1.1
Links

Tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.

Available Modules

module load SURVIVOR/1.0.6
Links

A robust and fast clustering method for amplicon-based studies. The purpose of swarm is to provide a novel clustering algorithm that handles massive sets of amplicons. Results of traditional clustering algorithms are strongly input-order dependent, and rely on an arbitrary global clustering threshold. swarm results are resilient to input-order changes and rely on a small local linking threshold d, representing the maximum number of differences between two amplicons.

Available Modules

module load swarm/3.1.4-GCC-11.3.0
Links

SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.

Available Modules

module load SWIG/4.0.2
Links

Perl module for reading and writing UniProtKB data in plain text format.

Available Modules

module load swissknife/1.80-GCC-9.2.0-Perl-5.30.1

Warning

Warning: swissknife/1.80-GCC-9.2.0-Perl-5.30.1 is old and marked for deletion. If you still need it, then please let us know.

Links

Szip compression software, providing lossless compression of scientific data

Available Modules

module load Szip/2.1-intel-2017a
Links

Generic indexer for TAB-delimited genome position files

Available Modules

module load tabix/0.2.6-GCC-11.3.0
Links

C++ wrapper to tabix indexer

Available Modules

module load tabixpp/1.1.2-GCC-11.3.0
Links

Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability.

Available Modules

module load tbb/2021.13.0-GCC-12.3.0
Links

Command-line program that automates the creation of sequence records for submission to GenBank

Available Modules

module load tbl2asn/20200519-linux64
Links

Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.

Available Modules

module load Tcl/8.5.19-gimkl-2017a
Links

An open-source software library for Machine Intelligence

Available Modules

module load TensorFlow/2.2.0-gimkl-2018b-Python-3.8.1
Links

NVIDIA TensorRT is a platform for high-performance deep learning inference

Available Modules

module load TensorRT/7.0.0.11-gimkl-2018b-Python-3.7.3
Links

Takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements.

Available Modules

module load TEtranscripts/2.2.3-gimkl-2022a
Links

Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.

Available Modules

module load Theano/1.0.5-gimkl-2020a-Python-3.8.2

Warning

Warning: Theano/1.0.5-gimkl-2020a-Python-3.8.2 is old and marked for deletion. If you still need it, then please let us know.

Links

Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.

Available Modules

module load Tk/8.6.9-GCCcore-7.4.0
Links

Prediction of transmembrane helices in proteins

Available Modules

module load TMHMM/2.0c
Links

tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.

Available Modules

module load tmux/2.8
Links

Implements a novel machine learning based paradigm to infer orthologous genes between related species and to accurately distinguish orthologs from paralogs or processed pseudogenes.

Available Modules

module load TOGA/1.1.4-gimkl-2022a-Python-3.11.3
Links

TransDecoder identifies candidate coding regions within transcript sequences.

Available Modules

module load TransDecoder/5.5.0-GCC-9.2.0-Perl-5.30.1
Links

TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.

Available Modules

module load TreeMix/1.13-GCC-11.3.0
Links

Locates tandem repeats in DNA sequences.

Available Modules

module load trf/4.04
Links

Tool for automated alignment trimming in large-scale phylogenetic analyses

Available Modules

module load trimAl/1.4.1-GCC-11.3.0
Links

A wrapper of FastQC and cutadapt to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files

Available Modules

module load TrimGalore/0.6.7-gimkl-2020a-Python-3.8.2-Perl-5.30.1
Links

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

Available Modules

module load Trimmomatic/0.39-Java-1.8.0_144
Links

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.

Available Modules

module load Trinity/2.8.4-gimkl-2017a.lua
Links

C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.

Available Modules

module load Trinotate/3.2.2-GCC-9.2.0
Links

Transfer RNA detection

Available Modules

module load tRNAscan-SE/2.0.7-GCC-9.2.0
Links

Tool for generating consensus long-read assemblies for bacterial genomes.

Available Modules

module load Trycycler/0.4.2-gimkl-2020a-Python-3.8.2
Links

Transcript Selector for BRAKER

Available Modules

module load TSEBRA/1.1.0-gimkl-2022a-Python-3.10.5
Links

TuiView is a lightweight raster GIS with powerful raster attribute table manipulation abilities.

Available Modules

module load TuiView/1.2.4-gimkl-2018b-Python-3.7.3
Links

Program Package For Electronic Structure Calculations.

Available Modules

module load TURBOMOLE/7.2.1-gompi-2022a
Links

TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads.

Available Modules

module load TurboVNC/2.2.4-GCC-9.2.0
Links

Nearly Infinite Neighbor Joining Application.

Available Modules

module load TWL-NINJA/0.97-cluster_only-GCC-9.2.0
Links

UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes.

Available Modules

module load UCC/1.2.0-GCCcore-12.3.0
Links

Unified Communication X An open-source production grade communication framework for data centric and high-performance applications

Available Modules

module load UCX/1.12.1-GCC-11.3.0
Links

UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.

Available Modules

module load UDUNITS/2.2.26-GCCcore-11.3.0
Links

Assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser.

Available Modules

module load Unicycler/0.4.8-gimkl-2020a-Python-3.8.2

Warning

Links

Fork of minimap2 optimized for assembly-to-reference alignment.

Available Modules

module load unimap/0.1-GCC-11.3.0

Warning

Warning: unimap/0.1-GCC-11.3.0 is old and marked for deletion. If you still need it, then please let us know.

Links

RAR is a powerful archive manager.

Available Modules

module load unrar/6.0.1-GCCcore-9.2.0
Links

USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

Available Modules

module load USEARCH/11.0.667-i86linux32
Links

Set of Linux utilities

Available Modules

module load util-linux/2.33-GCCcore-7.4.0
Links

Valgrind: Debugging and profiling tools

Available Modules

module load Valgrind/3.16.1-GCC-9.2.0
Links

Variant calling and somatic mutation/CNV detection for next-generation sequencing data

Available Modules

module load VarScan/2.4.4-Java-11.0.4
Links

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

Available Modules

module load VASP/6.4.2-intel-2022a
Links
Licence

VASP is proprietary software.

VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files.

Available Modules

module load VCF-kit/0.2.6-gimkl-2020a-Python-3.8.2
Links

Genetic variant detector designed to find polymorphisms smaller than the length of a short-read sequencing alignment.

Available Modules

module load vcflib/1.0.1-GCC-9.2.0
Links

The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.

Available Modules

module load VCFtools/0.1.14-gimkl-2018b-Perl-5.28.1
Links

Sequence assembler for very short reads

Available Modules

module load Velvet/1.2.10-GCC-9.2.0
Links

Perl script for optimising the three primary parameter options of the Velvet de novo sequence assembler.

Available Modules

module load VelvetOptimiser/2.2.5-GCC-9.2.0
Links

Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP.

Available Modules

module load VEP/104.3-GCC-9.2.0-Perl-5.30.1
Links

Hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads

Available Modules

module load verkko/2.0-Miniconda3
Links

variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods

Available Modules

module load vg/1.46.0
Links

Virus Identification By iteRative ANnoTation

Available Modules

module load VIBRANT/1.2.1-gimkl-2020a
Links

The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

Available Modules

module load ViennaRNA/2.4.17-gimkl-2020a
Links

Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set.

Available Modules

module load Vim/9.0.0500
Links

Tools for computing various oligonucleotide frequency (ONF) based distance/dissimialrity measures.

Available Modules

module load VirHostMatcher/1.0.0-gimkl-2020a
Links

VirSorter: mining viral signal from microbial genomic data.

Available Modules

module load VirSorter/1.0.6-gimkl-2020a-Perl-5.30.1
Links

VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration.

Available Modules

module load VirtualGL/2.6.2-gimkl-2020a

Warning

Warning: VirtualGL/2.6.2-gimkl-2020a is old and marked for deletion. If you still need it, then please let us know.

Links

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Available Modules

module load VMD/1.9.3-gimkl-2020a
Links

An open source alternative to the metagenomics tool USEARCH. Performs chimera detection, clustering, full-length and prefix dereplication, rereplication, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.

Available Modules

module load VSEARCH/2.4.3-gimkl-2017a

Warning

Warning: VSEARCH/2.4.3-gimkl-2017a is very old and will soon be removed, so please select a more recent version (try 'module spider VSEARCH').

Links

The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

Available Modules

module load VTK/7.1.1-gimkl-2018b-Python-2.7.16

Warning

Warning: VTK/7.1.1-gimkl-2018b-Python-2.7.16 is old and marked for deletion. If you still need it, then please let us know.

Links

Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.

Available Modules

module load VTune/2019_update4

Warning

Links

Workflow to Annotate Assemblies and Find LGT Events.

Available Modules

module load WAAFLE/0.1.0-gimkl-2022a-Python-3.10.5
Links

Wgsim is a small tool for simulating sequence reads from a reference genome.

Available Modules

module load wgsim/20111017-GCC-11.3.0
Links

Tool for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.

Available Modules

module load WhatsHap/1.6-gimkl-2022a-Python-3.10.5
Links

A built-package format for Python.

Available Modules

module load wheel/0.31.1-gimkl-2018b-Python-2.7.16
Links

Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques.

Available Modules

module load Winnowmap/2.03-GCC-11.3.0
Links

Aligning proteins or protein HMMs to DNA

Available Modules

module load Wise2/2.4.1-GCC-11.3.0
Links

de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies.

Available Modules

module load wtdbg/2.5-GCC-9.2.0
Links

widget toolkit and tools library for creating graphical user interfaces for cross-platform applications.

Available Modules

module load wxWidgets/3.1.4-GCC-9.2.0
Links

x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.

Available Modules

module load x264/20190226-GCCcore-7.4.0
Links

x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.

Available Modules

module load x265/3.5-GCC-11.3.0
Links

Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.

Available Modules

module load Xerces-C++/3.1.1-GCCcore-9.2.0

Warning

Warning: Xerces-C++/3.2.3-GCCcore-9.2.0 is old and marked for deletion. Please select a more recent version (try 'module spider Xerces-C++') or let us know that you still need it.

Links

Calls copy number variation (CNV) from normalized read-depth data from exome capture or other targeted sequencing experiments.

Available Modules

module load XHMM/1.0-gimkl-2018b

Warning

Warning: XHMM/1.0-gimkl-2018b is old and marked for deletion. If you still need it, then please let us know.

Links

keyboard keymap compiler and support library

Available Modules

module load xkbcommon/0.10.0-GCCcore-9.2.0
Links

Fast integrator of stochastic partial differential equations.

Available Modules

module load XMDS2/3.0.0-beta-gimkl-2020a-Python-3.8.2

Warning

Warning: XMDS2/3.0.0-beta-gimkl-2020a-Python-3.8.2 is old and marked for deletion. If you still need it, then please let us know.

Links

CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler. Provided with an XML instance specification (XML Schema), it generates C++ classes that represent the given vocabulary as well as XML parsing and serialization code. You can then access the data stored in XML using types and functions that semantically correspond to your application domain rather than dealing with the intricacies of reading and writing XML

Available Modules

module load XSD/4.0.0-GCCcore-7.4.0

Warning

Warning: XSD/4.0.0-GCCcore-7.4.0 is old and marked for deletion. If you still need it, then please let us know.

Links

xtb - An extended tight-binding semi-empirical program package.

Available Modules

module load xtb/6.6.1-foss-2023a
Links

xz: XZ utilities

Available Modules

module load XZ/5.2.4-GCCcore-7.4.0
Links

Chimeric Read Detector for long reads

Available Modules

module load yacrd/1.0.0-GCC-11.3.0
Links

Yet Another JSON Library. Why does the world need another C library for parsing JSON? Good question.

Available Modules

module load yajl/2.1.0-GCCcore-9.2.0
Links

Yet another k-mer analyzer

Available Modules

module load yak/0.1
Links

YAML parser and emitter in C++

Available Modules

module load yaml-cpp/0.6.2-GCCcore-7.4.0

Warning

Links

Yasm: Complete rewrite of the NASM assembler with BSD license

Available Modules

module load Yasm/1.3.0-GCCcore-7.4.0

Warning

Links

Yet Another eXchange Tool

Available Modules

module load YAXT/0.6.2-gimpi-2020a
Links

A theorem prover from Microsoft Research.

Available Modules

module load Z3/4.12.2-GCCcore-12.3.0
Links

ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply.

Available Modules

module load ZeroMQ/4.3.4-GCCcore-11.3.0
Links

Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality

Available Modules

module load Zip/3.0-GCCcore-9.2.0
Links

zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.

Available Modules

module load zlib/1.2.11
Links

Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.

Available Modules

module load zstd/1.5.2-GCCcore-11.3.0
Links

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