Software Catalog
The following catalog lists all software for which a module exists.
See the Installed Software Modules page for information about using
software listed here. Note that where module preloads are listed, all modules on
one line, and only one line, must be loaded before the module will be
available to load and use.
abinit
| Description |
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. |
| Versions |
10.0.9-ql5p3xd |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt openmpi/4.1.6-67ovor6 |
admixture
| Description |
ADMIXTURE is a tool for population ancestry analysis from multilocus SNP genotype datasets. |
| Versions |
1.3.0 |
| Keywords |
genomics, genetic ancestry, population genetics |
| Module preloads |
N/A |
afni
| Description |
AFNI suite of MRI neuroimaging tools binary tools only |
| Versions |
25.1.08 |
| Keywords |
fMRI, DTI, MRI, neuroimaging, neuroscience |
| Module preloads |
N/A |
afni-Rlibs
| Description |
AFNI suite of MRI neuroimaging tools and R libraries. |
| Versions |
25.1.08 |
| Keywords |
fMRI, DTI, MRI, neuroimaging, neuroscience |
| Module preloads |
N/A |
alphafold
| Description |
AlphaFold3 is an advanced deep learning model for protein structure prediction. |
| Versions |
3.0.1 |
| Keywords |
Bioinformatics, Protein Folding, Deep Learning, AI |
| Module preloads |
N/A |
amber
| Description |
Amber is a suite of biomolecular simulation programs. |
| Versions |
24 |
| Keywords |
biomolecular, simulation, mechanical, force fields, amber |
| Module preloads |
N/A |
aMeta
| Description |
aMeta is an ancient microbiome snakemake workflow. |
| Versions |
1.0.0 |
| Keywords |
bioinformatics, metagenomics, sequence analysis, workflow, snakemake |
| Module preloads |
N/A |
angsd
| Description |
Angsd is a program for analysing NGS data. |
| Versions |
0.935-4asngpy |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
ansys
| Description |
Electricity and Magnetism analsys. |
| Versions |
24.2 |
| Keywords |
Electronics analysis, GUI |
| Module preloads |
N/A |
ant
| Description |
A Java-based tool for automating software build processes. |
| Versions |
1.10.15 |
| Keywords |
Build Tool |
| Module preloads |
N/A |
ants
| Description |
Advanced Normalization Tools medical image registration toolkit. |
| Versions |
2.5.3 |
| Keywords |
normalization, brain structure, biomedical, image, registration, segmentation |
| Module preloads |
N/A |
apptainer
| Description |
Apptainer is a Singularity compatible container platform. |
| Versions |
1.3.4 |
| Keywords |
containers,apptainer,singularity |
| Module preloads |
N/A |
aspera
| Description |
IBM's proprietary solution for high-speed data transfer. |
| Versions |
4.2.12 |
| Keywords |
data transport |
| Module preloads |
N/A |
augustus
| Description |
Augustus predicts genes in eukaryotic genomic sequences. |
| Versions |
3.5.0-955ce17 |
| Keywords |
genetics, gene prediction, eukaryotic |
| Module preloads |
N/A |
autogen
| Description |
AutoGen is a tool for generating program files that contain repetitive text with varied substitutions. |
| Versions |
5.18.16 |
| Keywords |
Utility, development |
| Module preloads |
N/A |
bagel
| Description |
BAGEL is a parallel electronic-structure program. |
| Versions |
1.2.2 |
| Keywords |
electronic structure, quantum mechanics, simulation, chemistry |
| Module preloads |
oneapi/2024.2.1 |
bakta
| Description |
Bakta is a tool for the rapid and standardized annotation of bacterial genomes, MAGs, and plasmids. |
| Versions |
1.11.0 |
| Keywords |
bioinformatics, annotation, bacteria, MAG, plasmids |
| Module preloads |
N/A |
bamtools
| Description |
C++ API & command-line toolkit for working with BAM data. |
| Versions |
2.5.2-twq7d2p |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
bcftools
| Description |
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. |
| Versions |
1.19-iq5mwek |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
bedtools2
| Description |
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. |
| Versions |
2.31.1-xip5kr5 |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
bismark
| Description |
A tool to map bisulfite converted sequence reads and determine cytosine methylation states |
| Versions |
0.24.1-zmqux7v |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
blasr
| Description |
BLASR aligns long reads against a reference sequence. |
| Versions |
1.0 |
| Keywords |
genetics, bioinformatics, high-throughput sequencing, PacBio |
| Module preloads |
N/A |
blast-plus
| Description |
Basic Local Alignment Search Tool. |
| Versions |
2.14.1-ca7iit2 |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
blat
| Description |
BLAT performs extremely fast mRNA/DNA alignments and cross-species protein alignments. |
| Versions |
39x1 |
| Keywords |
genome, alignment, sequencing, bioinformatics, utility |
| Module preloads |
N/A |
boost
| Description |
Boost C++ library collection. |
| Versions |
1.89.0, 1.87.0, 1.85.0-bhfhhhm |
| Keywords |
Programming, C++, library |
| Module preloads |
gcc/13.3.0-xp3epyt
oneapi/2024.2.1 |
bowtie2
| Description |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences |
| Versions |
2.5.2-qd4omrm |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
bwa
| Description |
Burrow-Wheeler Aligner for pairwise alignment between DNA sequences. |
| Versions |
0.7.17-iqv3cxl |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
bwa-mem2
| Description |
BWA-MEM2 maps DNA sequences against a large reference genome, like the human genome. |
| Versions |
2.2.1 |
| Keywords |
genetics, sequence alignment |
| Module preloads |
N/A |
cactus
| Description |
Cactus is a reference-free whole-genome alignment program and pangenome graph construction toolkit. |
| Versions |
2.9.4 |
| Keywords |
bioinformatics, genomics, sequence analysis, pangenome, pipeline |
| Module preloads |
N/A |
cadence
| Description |
Electronic systems analysis. |
| Versions |
2024.10 |
| Keywords |
IC, VLSI, RF, PCB, routing, analog, digital, GUI |
| Module preloads |
N/A |
canu
| Description |
Canu is a single molecule sequence assembler for large and small genomes. |
| Versions |
2.3 |
| Keywords |
genetics, sequence assembler, assembly pipeline |
| Module preloads |
N/A |
cgal
| Description |
The Computational Geometry Algorithms Library (CGAL) is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics. |
| Versions |
5.6-ng5gssh |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
cgmlstfinder
| Description |
cgMLSTFinder runs KMA against a chosen cgMLST db |
| Versions |
1.2.0 |
| Keywords |
genomics, bioinformatics, sequence typing |
| Module preloads |
N/A |
cmake
| Description |
CMake is a cross-platform make system. |
| Versions |
3.31.8, 4.0.3 |
| Keywords |
Utility, programming, compiler |
| Module preloads |
N/A |
cuda
| Description |
CUDA compilers, libraries, and profiler tools. |
| Versions |
11.8.0, 12.2.2, 12.3.2, 12.4.1, 12.6.2, 12.9.1 |
| Keywords |
CUDA, gpu, library, programming, profiler |
| Module preloads |
N/A |
cudnn
| Description |
cuDNN libraries. |
| Versions |
8.9.7-cuda12, 9.12.0-cuda12, 9.4.0-cuda12 |
| Keywords |
CUDA, gpu, library, programming, cuDNN, deep learning, neural network |
| Module preloads |
N/A |
cutadapt
| Description |
Cutadapt finds and removes adapter sequences from high-throughput sequencing data. |
| Versions |
4.9 |
| Keywords |
Bioinformatics, Sequencing |
| Module preloads |
N/A |
dedalus
| Description |
Dedalus is a flexible framework for solving partial differential equations using spectral methods. |
| Versions |
3.0.3 |
| Keywords |
algebra, algebraic, partial differential equations, PDEs, fluid dynamics, spectral methods |
| Module preloads |
N/A |
deeptools
| Description |
Tools to process and analyze deep sequencing data. |
| Versions |
3.5.5 |
| Keywords |
bioinformatics, genomics, visualization, RNA-seq, next-generation sequencing, ChiP-seq |
| Module preloads |
N/A |
discovardenovo
| Description |
Discovar De Novo provides for de novo assembly of large and small genomes. |
| Versions |
52488 |
| Keywords |
Biology, assembly, ngs, sequencing |
| Module preloads |
N/A |
dmtcp
| Description |
dmtcp enables checkpointing of distributed and multi-threaded applications. |
| Versions |
3.1.2 |
| Keywords |
checkpointing |
| Module preloads |
N/A |
dnmtools
| Description |
Tools for analyzing DNA methylation data. |
| Versions |
1.4.4 |
| Keywords |
bioinformatics |
| Module preloads |
N/A |
dorado
| Description |
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. |
| Versions |
0.8.2, 1.0.2 |
| Keywords |
Nanopore, base read, sequencing, bioinformatics |
| Module preloads |
N/A |
eigen
| Description |
Eigen is a C++ template library for linear algebra matrices, vectors, numerical solvers, and related algorithms. |
| Versions |
3.4.0-auuuz67 |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
fastcat
| Description |
Fastcat is a utility to concatenate .fastq(.gz) files and create a summary of the sequences. |
| Versions |
0.22.1 |
| Keywords |
Bioinformatics formats, bam, fasta, fastq, fastlint, bamstats, bamindex |
| Module preloads |
N/A |
fastp
| Description |
A tool designed to provide fast all-in-one preprocessing for FastQ files. |
| Versions |
0.23.4-mjw7rak |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
fastplong
| Description |
Ultrafast preprocessing and quality control for long read sequencing data. |
| Versions |
0.2.0 |
| Keywords |
genetics, bioinformatics, sequencing |
| Module preloads |
N/A |
fastqc
| Description |
A quality control tool for high throughput sequence data. |
| Versions |
0.12.1-qxseug5 |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
fastsimcoal2
| Description |
Fastsimcoal2 provides fast sequential Markov coalescent simulation of genomic data under complex evolutionary models. |
| Versions |
2.8.0 |
| Keywords |
genetics, demographic inference, genomic simulation, evolutionary models |
| Module preloads |
N/A |
fasttree
| Description |
FastTree infers phylogenetic trees from alignments of nucleotide or protein sequences. |
| Versions |
2.1.11 |
| Keywords |
genomics, phylogenics, neighbor-joining, maximum-likelihood, sequence alignments |
| Module preloads |
N/A |
ffmpeg
| Description |
FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. |
| Versions |
7.0.2-43zjic5 |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
fftw
| Description |
Libraries for computation of discrete Fourier transform. |
| Versions |
3.3.10 |
| Keywords |
Library, Development, Core |
| Module preloads |
gcc/13.3.0-xp3epyt |
flye
| Description |
Flye is a de novo assembler for single-molecule sequencing reads using repeat graphs. |
| Versions |
2.9.6 |
| Keywords |
bioinformatics, metagenomics, genome assembly |
| Module preloads |
N/A |
freebayes
| Description |
Bayesian haplotype-based genetic polymorphism discovery and genotyping. |
| Versions |
1.3.6-r67va2b |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
freesurfer
| Description |
FreeSurfer MRI processing and analysis software. |
| Versions |
7.4.1 |
| Keywords |
MRI, neuroimaging, neuroscience |
| Module preloads |
N/A |
fsl
| Description |
FSL suite of MRI neuroimaging tools. |
| Versions |
6.0.7.14 |
| Keywords |
fMRI, DTI, neuroimaging, neuroscience |
| Module preloads |
N/A |
gatk
| Description |
The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. |
| Versions |
4.6.1.0 |
| Keywords |
genetics, variant discovery, genotyping, coverage analysis |
| Module preloads |
N/A |
gaussian
| Description |
Gaussian is an electronic structure program. |
| Versions |
16_C.02 |
| Keywords |
electronic structure, molecular |
| Module preloads |
N/A |
gcc
| Description |
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. |
| Versions |
13.3.0-xp3epyt |
| Keywords |
none provided |
| Module preloads |
N/A |
gdal
| Description |
GDAL is a translator library for raster and vector geospatial data formats. |
| Versions |
3.11.4, 3.9.2 |
| Keywords |
GIS, geospatial, raster, vector, graphics |
| Module preloads |
gcc/13.3.0-xp3epyt |
geos
| Description |
OpenGIS Simple Features for SQL spatial predicate functions and spatial operators. |
| Versions |
3.13.0, 3.14.0 |
| Keywords |
GIS, Geometry, OSGeo |
| Module preloads |
gcc/13.3.0-xp3epyt |
gromacs
| Description |
GROMACS performs Newtonian simulatons of molecular dynamics. |
| Versions |
2025.2 |
| Keywords |
molecular dynamics, chemistry, biochemistry |
| Module preloads |
gcc/13.3.0-xp3epyt
gcc/13.3.0-xp3epyt openmpi/5.0.5-ib |
gsl
| Description |
GNU scientific libraries |
| Versions |
2.8 |
| Keywords |
Programming, library, mathematics |
| Module preloads |
gcc/13.3.0-xp3epyt |
gubbins
| Description |
Gubbins provides rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. |
| Versions |
3.4 |
| Keywords |
recombination, alignment, phylogenetics |
| Module preloads |
N/A |
gurobi
| Description |
Gurobi optimization problem solver. |
| Versions |
12.0.1, 12.0.2 |
| Keywords |
Optimization, linear programming |
| Module preloads |
N/A |
gurobipy
| Description |
Gurobipy is the Python interface to the gurobi optimization problem solver. |
| Versions |
12.0.1-py3.11, 12.0.2-py3.11 |
| Keywords |
Optimization, linear programming |
| Module preloads |
N/A |
hcp-workbench
| Description |
Workbench is a visualization and discovery tool. |
| Versions |
2.0.1 |
| Keywords |
visualization, discovery, connectome, volume, surface, grayordinate |
| Module preloads |
N/A |
hdf5
| Description |
HDF5 data libraries and utilities. |
| Versions |
1.12.1, 1.14.4-3, 1.10.11 |
| Keywords |
Utility, programming, library |
| Module preloads |
gcc/13.3.0-xp3epyt
oneapi/2022.1.2 |
hello
| Description |
Hello world example of writing a module. |
| Versions |
1.0 |
| Keywords |
none provided |
| Module preloads |
N/A |
hifiasm
| Description |
Hifiasm is a fast haplotype-resolved de novo assembler |
| Versions |
0.25.0-r726 |
| Keywords |
Bioinformatics, telomere, de novo assembler, nanopore, haplotype |
| Module preloads |
N/A |
hisat2
| Description |
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome). |
| Versions |
2.2.1-x7h4grf |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
hoomd-blue
| Description |
HOOMD-blue is a general-purpose particle simulation toolkit. |
| Versions |
5.0.1 |
| Keywords |
particle simulation, molecular dynamics, Monte Carlo, chemistry |
| Module preloads |
gcc/13.3.0-xp3epyt openmpi/5.0.5 |
htslib
| Description |
C library for high-throughput sequencing data formats. |
| Versions |
1.19.1-6ivqauw |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
igv
| Description |
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, and genomic annotations. |
| Versions |
2.16.2-7fat2jl |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
ipopt
| Description |
Ipopt is a software package for large-scale nonlinear optimization. |
| Versions |
3.14.17 |
| Keywords |
library, nonlinear optimization, mathematics |
| Module preloads |
gcc/13.3.0-xp3epyt |
iqtree2
| Description |
IQ-TREE 2 is a software package for phylogenomic inference using maximum likelihood. |
| Versions |
2.3.6 |
| Keywords |
genetics, phylogenomic inference, reports, maximum likelihood |
| Module preloads |
N/A |
itk
| Description |
itk is an open-source system for medical image processing. |
| Versions |
5.4.0 |
| Keywords |
library, development, image processing, MRI |
| Module preloads |
gcc/13.3.0-xp3epyt |
jags
| Description |
JAGS is a program for analysis of Bayesian hierarchical models. |
| Versions |
4.3.2 |
| Keywords |
Bayesian, Markov, MCMC, build tools, mathematics |
| Module preloads |
N/A |
julia
| Description |
Julia is a high-level, high-performance dynamic language for technical computing. |
| Versions |
1.10.5 |
| Keywords |
Programming |
| Module preloads |
N/A |
kmers-gwas
| Description |
kmersGWAS is a library for genome-wide associations using k-mers. |
| Versions |
0.2-beta, 0.3-beta |
| Keywords |
genetics, bioinformatics, genome-wide association studies |
| Module preloads |
N/A |
kraken2
| Description |
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. |
| Versions |
2.1.3-5jimqoc |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
lammps
| Description |
LAMMPS is a classical molecular dynamics code that models an ensemble of particles. |
| Versions |
29Aug2024, 29Aug2024-gpu, 29Aug2024-kokkos |
| Keywords |
molecular dynamics |
| Module preloads |
gcc/13.3.0-xp3epyt openmpi/5.0.5-ib
gcc/13.3.0-xp3epyt openmpi/5.0.5 |
lapack
| Description |
LAPACK is a software library that provides routines for solving linear algebra problems. |
| Versions |
3.12.0 |
| Keywords |
Libraries, linear algebra |
| Module preloads |
gcc/13.3.0-xp3epyt |
launcher
| Description |
A framework for running lots of short serial commands; alternative to job arrays. |
| Versions |
3.7 |
| Keywords |
Parallel, job array, many short jobs |
| Module preloads |
N/A |
llama.cpp
| Description |
llama.cpp is an open-source software library that performs inference on LLMs. |
| Versions |
b3933-cuda, b4793-cuda |
| Keywords |
Inference, large language models, LLM tool |
| Module preloads |
N/A |
macs2
| Description |
Loads python package MACS2 (Model-based Analysis of ChIP-Seq data) |
| Versions |
2.2.9.1 |
| Keywords |
Bioinformatics, ChIP-Seq, Data Analysis |
| Module preloads |
N/A |
magma
| Description |
Magma does computations in algebra, number theory, algebraic geometry, and algebraic combinatorics. |
| Versions |
2.28-14-cuda11 |
| Keywords |
algebra, number theory, algebraic, geometry, combinatorics |
| Module preloads |
N/A |
mathematica
| Description |
Mathematical and technical computing package. |
| Versions |
14.1 |
| Keywords |
mathematics, algebra, wolfram |
| Module preloads |
N/A |
matlab
| Description |
Matlab programming environment. |
| Versions |
R2023b, R2024b, R2025b |
| Keywords |
Mathematics, programming, simulation |
| Module preloads |
N/A |
maven
| Description |
Maven is a tool for building and managing Java-based projects. |
| Versions |
3.9.9 |
| Keywords |
Build Tool |
| Module preloads |
N/A |
minimap2
| Description |
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Mappy provides a convenient interface to minimap2. |
| Versions |
2.28-qcu5ixf |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
mkl
| Description |
Intel oneAPI optimized BLAS/LAPACK libraries, including FFT and other mathematical and statistical routines. |
| Versions |
2024.2 |
| Keywords |
Library, Development, Core, BLAS, LAPACK |
| Module preloads |
N/A |
mosek
| Description |
MOSEK is an optimization solver for large-scale mathematical optimization problems. |
| Versions |
11.0.28 |
| Keywords |
optimization solver, mathematical, sparse problems |
| Module preloads |
N/A |
namd
| Description |
NAMD is a molecular dynamics code for high-performance simulation of large biomolecular systems. |
| Versions |
3.0.1-cuda |
| Keywords |
molecular dynamics, simulation, free energy calculations |
| Module preloads |
N/A |
nanoq
| Description |
Nanoq provides filters and summary reports for nanopore reads |
| Versions |
0.10.0 |
| Keywords |
genetics, quality control, reports, nanopore reads |
| Module preloads |
N/A |
netcdf-c
| Description |
Libraries for creating and manipulating NetCDF files. |
| Versions |
4.9.2, 4.9.3 |
| Keywords |
Library, Development, Core |
| Module preloads |
gcc/13.3.0-xp3epyt
gcc/13.3.0-xp3epyt openmpi/5.0.7 |
netcdf-cxx
| Description |
C++ API to the NetCDF-C libraries. |
| Versions |
4.3.1 |
| Keywords |
Library, Development, Core |
| Module preloads |
gcc/13.3.0-xp3epyt |
netcdf-fortran
| Description |
Libraries for creating and manipulating NetCDF files using Fortran. |
| Versions |
4.6.1, 4.6.2 |
| Keywords |
Library, Development, Core |
| Module preloads |
gcc/13.3.0-xp3epyt |
nextflow
| Description |
Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. |
| Versions |
24.10.2, 25.04.3 |
| Keywords |
pipeline, dataflow, workflow, bioinformatics |
| Module preloads |
N/A |
ngstools
| Description |
ngsTools is a set of programs for population genetics analyses of NGS data. |
| Versions |
b38ea27 |
| Keywords |
bioinformatics, population genetics, NGS |
| Module preloads |
N/A |
ollama
| Description |
Ollama LLM interface |
| Versions |
0.9.0 |
| Keywords |
LLM |
| Module preloads |
N/A |
oneapi
| Description |
Intel compiler suite, libraries, and MPI |
| Versions |
2022.1.2, 2024.2.1 |
| Keywords |
Compiler, programming, development |
| Module preloads |
N/A |
openblas
| Description |
BLAS provides standard interfaces for linear algebra, including vector-vector operations, matrix-vector operations, and matrix-matrix operations. |
| Versions |
0.3.28 |
| Keywords |
Programming, C++, library |
| Module preloads |
gcc/13.3.0-xp3epyt |
openjdk
| Description |
OpenJDK is a free and open-source implementation of the Java Platform. |
| Versions |
1.8.0, 23.0.0 |
| Keywords |
Java, programming |
| Module preloads |
N/A |
openmolcas
| Description |
OpenMolcas is a quantum chemistry software package. |
| Versions |
25.02 |
| Keywords |
quantum chemistry, physics, electronic structure |
| Module preloads |
gcc/13.3.0-xp3epyt
gcc/13.3.0-xp3epyt openmpi/5.0.7 |
openmpi
| Description |
OpenMPI implementation of the MPI protocol |
| Versions |
5.0.5-ib, 5.0.7, 4.1.6-67ovor6 |
| Keywords |
Utility, Development, Core |
| Module preloads |
gcc/13.3.0-xp3epyt |
orca
| Description |
ORCA is a quantum chemistry package providing methods in electronic structure theory. |
| Versions |
6.0.1, 6.1.0 |
| Keywords |
quantum, chemistry, electronic, theory, DFT, ab initio, SCF-MO, quantum chemistry |
| Module preloads |
gcc/13.3.0-xp3epyt openmpi/5.0.5 |
paraview
| Description |
ParaView is a post-processing visualization engine. |
| Versions |
5.13.1 |
| Keywords |
Visualization engine, GUI |
| Module preloads |
N/A |
patric
| Description |
PATRIC is a set of data and software tools for bacterial pathogen research. |
| Versions |
1.039 |
| Keywords |
genetics, gene annotation, genome, bacteria |
| Module preloads |
N/A |
pblat
| Description |
pblat is a multithreaded BLAT algorithm, speeding up aligning sequences to genomes. |
| Versions |
2.5.1 |
| Keywords |
genome, alignment, sequencing, bioinformatics, utility |
| Module preloads |
N/A |
pcangsd
| Description |
PCAngsd is a framework for analyzing low depth NGS data in heterogeneous populations using PCA. |
| Versions |
1.2, 1.36.1 |
| Keywords |
bioinformatics, genomics, next-generation sequencing, NGS, PCA |
| Module preloads |
N/A |
perl5libs
| Description |
perl5libs provides a collection of Perl modules, including bioperl. |
| Versions |
5.32.1 |
| Keywords |
Perl, modules, tools, bioinformatics, genomics |
| Module preloads |
N/A |
phdf5
| Description |
Parallel HDF5 data libraries and utilities. |
| Versions |
1.14.4-3 |
| Keywords |
Utility, programming, library |
| Module preloads |
gcc/13.3.0-xp3epyt openmpi/5.0.7 |
phonopy
| Description |
Phonopy is a python package for phonon calculations at harmonic and quasi-harmonic levels. |
| Versions |
2.43.2 |
| Keywords |
phonons, computational chemistry, materials science |
| Module preloads |
N/A |
picard
| Description |
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. |
| Versions |
3.1.1-otrgwkh |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
plasmidfinder
| Description |
PlasmidFinder identifies plasmids in total or partial sequenced isolates of bacteria. |
| Versions |
2.1.6 |
| Keywords |
genomics, plasmids, bacteria, sequencing, bioinformatics |
| Module preloads |
N/A |
plink
| Description |
PLINK is a free, open-source whole genome association analysis toolset. |
| Versions |
1.07, 1.9b7.7 |
| Keywords |
genetics, genome association, sequencing, bioinformatics |
| Module preloads |
N/A |
pops
| Description |
The POPS program performs inference of ancestry distribution models. |
| Versions |
1.2.1 |
| Keywords |
population genetics, evolutionary genomics, Bayesian clustering |
| Module preloads |
N/A |
proj
| Description |
PROJ is a generic coordinate transformation software. |
| Versions |
9.5.0, 9.6.2 |
| Keywords |
GIS, Library |
| Module preloads |
gcc/13.3.0-xp3epyt |
prokka
| Description |
Prokka is a tool for rapid prokaryotic genome annotation. |
| Versions |
1.14.6 |
| Keywords |
genetics, genome annotation, gene finding, functional assignment, bacterial genomes |
| Module preloads |
N/A |
py-htseq
| Description |
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. |
| Versions |
2.0.3-mb7ap7s |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
py-multiqc
| Description |
MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It is written in Python and contains modules for a large number of common bioinformatics tools. |
| Versions |
1.15-fmpaaj7 |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
pyscf
| Description |
PySCF is a collection of electronic structure programs powered by Python. |
| Versions |
2.8.0 |
| Keywords |
quantum chemistry, electronic structure, materials science |
| Module preloads |
N/A |
python3.10-anaconda
| Description |
Python Data Science Distribution |
| Versions |
2023.03-1 |
| Keywords |
Python, Programming, Scripting, numpy, scipy, matplotlib, ipython, jupyter |
| Module preloads |
N/A |
python3.11-anaconda
| Description |
Python Data Science Distribution |
| Versions |
2024.02-1 |
| Keywords |
Python, Programming, Scripting, numpy, scipy, matplotlib, ipython, jupyter |
| Module preloads |
N/A |
python3.12-anaconda
| Description |
Python Data Science Distribution |
| Versions |
2024.06-1 |
| Keywords |
Python, Programming, Scripting, numpy, scipy, matplotlib, ipython, jupyter |
| Module preloads |
N/A |
python3.9-anaconda
| Description |
Python Data Science Distribution |
| Versions |
2022.10 |
| Keywords |
Python, Programming, Scripting, numpy, scipy, matplotlib, ipython, jupyter |
| Module preloads |
N/A |
qiime2
| Description |
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis pipeline. |
| Versions |
2024.10-amplicon, 2024.10-metagenome |
| Keywords |
genetics, microbiome, analysis, pipeline |
| Module preloads |
N/A |
quantum-espresso
| Description |
Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. |
| Versions |
7.3.1-szp4t4s |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt openmpi/4.1.6-67ovor6 |
quantumatk
| Description |
Atomistic Simulation Software. |
| Versions |
2023.12 |
| Keywords |
Atomistic analysis, GUI |
| Module preloads |
N/A |
R
| Description |
R environment for statistical computing and graphics |
| Versions |
4.4.1, 4.5.1 |
| Keywords |
Statistics, graphics, big data, data science |
| Module preloads |
N/A |
Rgeospatial
| Description |
A collection of R geospatial libraries |
| Versions |
4.4.1-2024-10-02, 4.5.1-2025-08-21, 4.5.1-2025-09-26 |
| Keywords |
Statistics, graphics, big data, data science, geospatial, geography, spatial, map |
| Module preloads |
N/A |
roary
| Description |
Roary is a tool for rapid large-scale prokaryote pan genome analysis. |
| Versions |
3.13.0 |
| Keywords |
bioinformatics, genomics, sequencing, pathogens |
| Module preloads |
N/A |
rstudio
| Description |
RStudio Desktop is a graphichal user interface for R. |
| Versions |
2024.09.0, 2025.05.1 |
| Keywords |
Statistics, graphics, big data, data science, IDE |
| Module preloads |
N/A |
Rtidyverse
| Description |
R Tidyverse environment for statistical computing and graphics |
| Versions |
4.4.1, 4.5.1 |
| Keywords |
Statistics, graphics, big data, data science, tidyverse |
| Module preloads |
N/A |
s-metro
| Description |
Assessment of numerical and image based metrology. |
| Versions |
2024.06 |
| Keywords |
Atomistic analysis, GUI |
| Module preloads |
N/A |
salmon
| Description |
Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. |
| Versions |
1.10.2-uhrt76c |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
sambamba
| Description |
Sambamba is a high performance tool for working with SAM and BAM files. |
| Versions |
1.0.1 |
| Keywords |
bioinformatics, sam, bam, sequence alignment, genomics |
| Module preloads |
N/A |
samtools
| Description |
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format |
| Versions |
1.19.2-pfmpoam |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
sentaurus
| Description |
Process and Device simulation tools. |
| Versions |
2024.03 |
| Keywords |
semiconductor, process, device, analysis, simulation, GUI |
| Module preloads |
N/A |
seqkit
| Description |
Toolkit for FASTA/Q file manipulation. |
| Versions |
2.9.0 |
| Keywords |
file manipulation, FASTA/Q, toolkit |
| Module preloads |
N/A |
silicon-workbench
| Description |
Hierarchical layout visualization and analysis tool. |
| Versions |
2023.09 |
| Keywords |
layout visualization, analysis, gsdii, oasis, s-litho, s-metro, tcad, GUI |
| Module preloads |
N/A |
slim
| Description |
SLiM is an evolutionary simulation framework. |
| Versions |
4.3, 5.0 |
| Keywords |
genetics, evolutionary simulations, graphical interface |
| Module preloads |
N/A |
snippy
| Description |
Snippy is a tool for rapid haploid variant calling and core genome alignment. |
| Versions |
4.6.0 |
| Keywords |
bioinformatics, genomics, haploid, snps, alignment |
| Module preloads |
N/A |
snp-sites
| Description |
SNP-sites finds SNP sites from a multi-FASTA alignment file. |
| Versions |
2.5.1 |
| Keywords |
bioinformatics, genomics, pathogen, sequencing |
| Module preloads |
N/A |
snpeff
| Description |
SnpEff is a variant annotation and effect prediction tool. |
| Versions |
5.2c |
| Keywords |
Genetic Variant Annotation |
| Module preloads |
N/A |
spss
| Description |
SPSS is a powerful statistical software suite for data analysis and graphics. |
| Versions |
27 |
| Keywords |
statistics, econometrics |
| Module preloads |
N/A |
sqlite
| Description |
SQLite is an SQL database engine in a C library. |
| Versions |
3.46.1, 3.50.4 |
| Keywords |
database engine, embedded, relational, SQL |
| Module preloads |
gcc/13.3.0-xp3epyt |
sratoolkit
| Description |
The NCBI SRA Toolkit enables reading ('dumping') of sequencing files from the SRA database and writing ('loading') files into the .sra format. |
| Versions |
3.0.0-y2rspiu |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
star
| Description |
STAR is an ultrafast universal RNA-seq aligner. |
| Versions |
2.7.11a-cp575va |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
subread
| Description |
Subread provides a set of high-performance read alginment, quantification and mutation tools for sequencing data. |
| Versions |
2.0.8 |
| Keywords |
genetics, sequence alignment, sequence analysis, bioinformatics |
| Module preloads |
N/A |
tbb
| Description |
Intel oneAPI Thread Building Blocks. |
| Versions |
2021.13 |
| Keywords |
Library, development, core, thread |
| Module preloads |
N/A |
tetools
| Description |
TE Tools provides the Dfam Transposable Element tools. |
| Versions |
1.93 |
| Keywords |
bioinformatics, genomics, sequencing, transposable elements, TEs |
| Module preloads |
N/A |
trimgalore
| Description |
Trim Galore! is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. |
| Versions |
0.6.10-namgrp2 |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
trimmomatic
| Description |
A flexible read trimming tool for Illumina NGS data. |
| Versions |
0.39-vdnktze |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |
use.own
| Description |
Module to add personal module directory to module path. |
| Versions |
N/A |
| Keywords |
none provided |
| Module preloads |
N/A |
valgrind
| Description |
Valgrind is a programming tool for memory debugging, memory leak detection, and profiling. |
| Versions |
3.23.0 |
| Keywords |
Debugging, Profiling Memory, Debugging, Leak Detection, Profiling |
| Module preloads |
N/A |
varscan
| Description |
VarScan - Variant calling software |
| Versions |
2.4.6 |
| Keywords |
Bioinformatics, Genomics |
| Module preloads |
N/A |
vcf2maf
| Description |
vcf2maf converts a VCF into MAF, where each variant is annotated to only one of all possible gene isoforms. |
| Versions |
1.6.22 |
| Keywords |
genetics, annotation, variants, utility |
| Module preloads |
N/A |
vcflib
| Description |
vcflib is both a C++ library and cmdline tools for parsing and manipulating VCF files. |
| Versions |
1.0.12 |
| Keywords |
bioinformatics, genomics, VCF |
| Module preloads |
N/A |
vcftools
| Description |
VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. |
| Versions |
0.1.16 |
| Keywords |
none provided |
| Module preloads |
N/A |
vep
| Description |
VEP is a tool for predicting the functional effects of genomic variants. |
| Versions |
113.4 |
| Keywords |
bioinformatics, genomics, variants |
| Module preloads |
N/A |
vtk
| Description |
The Visualization Toolkit (VTK) for scientific visualization and analysis. |
| Versions |
9.4.0 |
| Keywords |
visualization, imaging, rendering |
| Module preloads |
gcc/13.3.0-xp3epyt |
xtb
| Description |
Semiempirical extended tight binding program package |
| Versions |
6.6.0-ivf4oeb |
| Keywords |
none provided |
| Module preloads |
gcc/13.3.0-xp3epyt |