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Listes des applications

Ces applications sont disponibles sur toutes les ressources HPC2 via modules LMOD.

Name Description Available versions (requirements)
abinit ABINIT: a program to find the total energy, charge density and electronic structure of systems made of electrons and nuclei 7.10.5 (gcc/4.8.4, openmpi/1.8.4)
abyss ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. 1.9.0 (gcc/4.8.4, openmpi/1.8.4), 2.2.1 (gcc/8.1.0)
ambertools Amber is a suite of biomolecular simulation programs. 19.0.0 (gcc/8.1.0)
amos A Modular, Open-Source whole genome assembler. 3.1.0 (gcc/4.8.4)
AmpliconNoise A python front end for Chris Quince's AmpliconNoise c code. 1.27 (gcc/4.8.4)
ant 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. 1.10.1
asgal ASGAL (Alternative Splicing Graph ALigner) is a tool for detecting the alternative splicing events expressed in a RNA-Seq sample with respect to a gene annotation. 104c19b (python/3.7.1, gcc/8.1.0)
bamtools bamtools, command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. 2.5.1 (gcc/8.1.0)
bbtools BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. 37.97
bcftools BCFtools are meant as a faster replacement for most of the perl VCFtools commands 1.9 (gcc/8.1.0)
beagle beagle, general purpose library for evaluating the likelihood of sequence evolution on trees 3.1.2 (gcc/8.1.0)
BEAST BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. 1.10.4, 2.5.2
bedtools bedtools: a fast and flexible toolset for genome arithmetic 2.25.0 (gcc/4.8.4), 2.27.1 (gcc/4.8.4), 2.30.0 (gcc/8.1.0)
bioconductor : Bioconductor: Tools for the analysis and comprehension of high-throughput genomic data using the R statistical programming language 3.2 (gcc/4.8.4)
biom-format BIOM: Biological Observation Matrix. 2.1.6 (gcc/4.8.4)
bioperl BioPerl: a collection of Perl modules for bioinformatics applications 1.7.0_RC5 (Release Candidate)
biopython BioPython: a set of freely available tools for biological computation written in Python 1.65 (gcc/4.8.4), 1.65 (gcc/4.8.4, python/3.4.5), 1.77 (python/3.7.1, gcc/8.1.0)
bitarray efficient arrays of booleans. 0.8.1 (gcc/4.8.4)
blast-legacy Blast: legacy executables of blast 2.2.26
boost Boost: free peer-reviewed portable C++ source libraries 1.59.0 (intel/2018.1), 1.59.0 (gcc/4.8.4), 1.59.0 (gcc/8.1.0)
boost-mpi Boost.MPI: a C++ library for message passing in high-performance parallel applications. 1.59.0 (gcc/4.8.4, openmpi/1.8.4)
bowtie2 Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. 2.3.2, 2.3.4.3
bowtie Bowtie: Ultrafast, memory-efficient short read aligner 1.1.2 (gcc/4.8.4), 1.2.1.1 (gcc/4.8.4)
breakdancer BreakDancer provides genome-wide detection of structural variants from next generation paired-end sequencing reads. 1.4.5
busco BUSCO, Assessing Genome Assembly and Annotation Completeness 5.0.0
bwa BWA: Burrow-Wheeler Aligner for pairwise alignment between DNA sequences 0.7.12 (gcc/8.1.0), 0.7.12 (gcc/4.8.4), 0.7.17 (gcc/8.1.0)
cadmesh CADMesh is a direct CAD model import interface for GEANT4 leveraging ASSIMP for reading the CAD files. 1.0 (gcc/4.8.4)
cast3m Cast3M is a computer code for the analysis of structures by the finit element method and the Computational Fluids Dynamics. 16.1, 17.0
cdbfasta Constant DataBase tools for indexing and retrieving records from multi-FASTA or similarly structured files. cdb64 (gcc/4.8.4)
cdhit CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. 4.6.8 (gcc/4.8.4)
cDNA_Cupcake cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data. 12.5 (python/3.7.1, gcc/8.1.0)
cgal CGAL: efficient and reliable geometric algorithms in the form of a C++ library 4.7 (gcc/4.8.4), 4.12 (gcc/8.1.0), 4.12 (gcc/4.8.4)
clearcut Clearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. 1.0.9 (gcc/4.8.4)
clhep CLHEP A Class Library for High Energy Physics 2.4.1.0 (gcc/4.8.4), 2.4.1.0 (gcc/8.1.0)
ClustalOmega Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. 1.2.4
cmake CMake is an open-source, cross-platform family of tools designed to build, test and package software. 3.6.1, 3.13.4, 3.21.5
cnvnator CNVnator, a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads 0.3.3 (gcc/8.1.0)
comsol COMSOL Multiphysics is a general-purpose simulation software for modeling designs, devices, and processes in all fields of engineering, manufacturing, and scientific research. 5.4, 5.6
conda conda: Miniconda3 python environment. 4.10.3, 4.12.0, 23.3.1
cpop CPOP: a cell population C++ library based on Geant4 2.0 (gcc/8.1.0)
crri Default modules automatically loaded. (no specific version)
cuda The NVIDIA CUDA Toolkit provides a development environment for creating high performance GPU-accelerated applications. 9.2.148, 10.0.130, 10.2.89, 11.2.152, 11.6.2, 12.0.1
cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. 2.2.1
cutadapt Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads 1.18 (gcc/8.1.0)
cython The Cython compiler for writing C extensions for the Python language. 0.25.2 (gcc/4.8.4), 0.29.14 (python/3.7.1, gcc/8.1.0)
deeploc DeepLoc, Prediction of eukaryotic protein subcellular localization using deep learning. 1.0 (gcc/8.1.0)
deepTools User-friendly tools for exploring deep-sequencing data 3.1.2 (gcc/4.8.4)
diamond DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. 0.9.8, 2.0.5
dRep dRep is a python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set. (gcc/8.1.0), 3.0.0 (gcc/8.1.0)
ea-utils Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. 1.1.2-537 (gcc/4.8.4)
edirect Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. 1.0
eigen Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. 3.3.1 (gcc/4.8.4)
emboss EMBOSS: a free Open Source software analysis package specially developed for the needs of the molecular biology 6.5.7 (gcc/8.1.0), 6.5.7 (gcc/4.8.4)
emirge EMIRGE reconstructs full length sequences from short sequencing reads 0.61.1 (gcc/4.8.4)
exonerate a generic tool for sequence alignment. 2.4.0 (gcc/4.8.4)
extracthifi extracthifi is used to extract PacBio HiFi reads (>= Q20) from full CCS output. 1.0.0
fastANI fast alignment-free computation of whole-genome Average Nucleotide Identity. 1.0
fastqc A quality control tool for high throughput sequence data. 0.11.4, 0.11.7
fastspar Rapid and scalable correlation estimation for compositional data 0.0.9_meso (gcc/8.1.0)
FastTreeMP FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. 2.1.10 (gcc/4.8.4)
fastx-toolkit FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. 0.0.13
fftw FFTW: library for computing the discrete Fourier transform (DFT) in one or more dimensions 3.3.4 (gcc/4.8.4), 3.3.4 (gcc/8.1.0)
finishm FinishM attempts to improve draft genomes by considering the computational problem to be about finishing, not assembly in the traditional sense. 0.0.9 (gcc/4.8.4)
flye Flye is a de novo assembler for single molecule sequencing reads. 2.9 (python/3.7.1, gcc/8.1.0)
fqtools fqtools is a software suite for fast processing of FASTQ files. 2.0 (gcc/8.1.0), 2.3 (gcc/8.1.0)
freebayes freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. 1.3.1
gate GATE: opensource software dedicated to numerical simulations in medical imaging and radiotherapy 7.2 (gcc/4.8.4), 8.0 (gcc/4.8.4), 8.1.p01_cpop (gcc/8.1.0), 8.1.p01 (gcc/4.8.4), 8.1.p01 (gcc/8.1.0), 8.2 (gcc/8.1.0), 9.1 (gcc/8.1.0), 9.3 (gcc/10.2.0)
gatk GATK : Genome Analysis Toolkit 4.1.0.0 (gcc/8.1.0)
gcc GCC: GNU Compiler Collection (C, C++, FORTRAN) 8.1.0, 10.2.0, 4.8.4
gdal GDAL : translator library for raster and vector geospatial data formats 2.3.2 (gcc/8.1.0)
geant4 Geant4: a toolkit for the simulation of the passage of particles through matter 10.07.p01_mt (gcc/8.1.0), 10.07.p01 (gcc/8.1.0), 11.1.1_mt (gcc/10.2.0), 11.1.1 (gcc/10.2.0)
genometools The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. 1.5.9 (gcc/4.8.4)
geos GEOS : Geometry Engine - Open Source is a C++ port of the ​Java Topology Suite (JTS). 3.3.3 (gcc/4.8.4), 3.7.0 (gcc/8.1.0)
ggplot2 : ggplot2: plotting system for R, based on the grammar of graphics 2.2.1 (gcc/4.8.4)
ghc GHC is a state-of-the-art, open source, compiler and interactive environment for the functional language Haskell. 8.2.2 (gcc/4.8.4)
gmap A Genomic Mapping and Alignment Program for mRNA and EST Sequences. 20180530 (gcc/4.8.4), 20200408 (gcc/8.1.0)
goofys a high-performance, POSIX-ish Amazon S3 file system written in Go 0.19.0, 0.19.0
gromacs 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. 2016.1 (gcc/4.8.4), 2020.6_cuda (gcc/8.1.0), 2020.6 (gcc/8.1.0), 2020.7 (gcc/10.2.0)
gsl The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. 1.9 (gcc/4.8.4), 2.6 (gcc/8.1.0)
hdf5 HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. 1.8.18 (gcc/8.1.0), 1.8.18 (gcc/4.8.4)
hifiasm Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. 0.12 (gcc/8.1.0), 0.15.2 (gcc/8.1.0), 0.16.1 (gcc/8.1.0)
HISAT2 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads against the general human population. 2.0.5
hmat A hierarchical matrix C/C++ library including a LU solver. 1.5.0 (gcc/4.8.4)
hmmer HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. 3.1b2
HMMER2GO HMMER2GO is a command line application to map DNA sequences, typically transcripts, to Gene Ontology based on the similarity of the query sequences to curated HMM models for protein families represented in Pfam. 0.17.9, 0.18.0
HOMER Software for motif discovery and next-gen sequencing analysis. 4.11
HTSeq HTSeq : Python package that provides infrastructure to process data from high-throughput sequencing assays. 0.11.2 (gcc/8.1.0)
htslib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. 1.9 (gcc/8.1.0)
idba IDBA: a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics 1.1.2 (gcc/4.8.4)
IM-Tornado IM-TORNADO: A pipeline for 16S reads from paired-end libraries. 2.0.3.3
infernal Infernal - INFERence of RNA ALignment - is for searching DNA sequence databases for RNA structure and sequence similarities. 1.1.1 (gcc/4.8.4), 1.1.2 (gcc/4.8.4)
intel Intel Compilers for C/C++ and Fortran 2018.1
intel-cpu-opencl OpenCL Runtimes for Intel Processors allows Executing OpenCL kernels directly on Intel CPUs as OpenCL target devices. 18.1.0.014
interproscan InterProScan, genome-scale protein function classification 5.52-86.0
ipp Intel Integrated Primitives offers developers high-quality, production-ready, low-level building blocks for image processing, signal processing, and data processing applications. 2018.1 (intel/2018.1)
ipython Productive Interactive Computing 3.1.0 (gcc/4.8.4)
ITK Insight Segmentation and Registration Toolkit 4.13.0 (gcc/4.8.4)
ITSx ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing. 1.0.11
jasper 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 (i.e., ISO/IEC 15444-1). 2.0.0 (gcc/4.8.4)
java Java: Java Development Kit 8 from Oracle oracle-1.7.0_79, oracle-1.11.0_11, oracle-1.8.0_45
jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. 2.2.10
kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. 1.3.0 (gcc/8.1.0)
kronatools KronaTools: a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. 2.6
llvm LLVM: Libraries providing a modern source- and target-independent optimizer, along with code generation support 3.6.2 (gcc/4.8.4)
lmdb LMDB, an ultra-fast, ultra-compact, crash-proof key-value embedded data store. 0.29.4 (gcc/8.1.0)
lmod Lmod: An Environment Module System
MACS2 Model-based Analysis of ChIP-Seq 2.1.0_20150420 (gcc/4.8.4), 2.1.2 (gcc/4.8.4)
MACS3 Model-based Analysis of ChIP-Seq 3.0.0a6 (gcc/8.1.0)
MAFFT MAFFT is a multiple sequence alignment program for unix-like operating systems. 7.427 (gcc/8.1.0)
malt malt, MEGAN alignment tool 0.4.3
mapDamage mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. 2.0.9 (gcc/8.1.0)
mash Fast genome and metagenome distance estimation using MinHash. 2.0, 2.3
MaSuRCA The MaSuRCA (Maryland Super Read Cabog Assembler) assembler combines the benefits of deBruijn graph and Overlap-Layout-Consensus assembly approaches. 3.3.4 (gcc/8.1.0)
matlab-runtime Matlab Runtime environment 2017b.v93
matplotlib matplotlib: 2D plotting library 1.4.3 (gcc/4.8.4), 1.4.3 (gcc/4.8.4, python/3.4.5), 1.5.3 (gcc/4.8.4), 3.4.1 (python/3.7.1, gcc/8.1.0)
MDAnalysis MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. 0.16.2 (gcc/4.8.4), 0.18.0 (gcc/4.8.4)
megahit MEGAHIT, An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. 1.1.1 (gcc/4.8.4), 1.2.9 (gcc/8.1.0)
meshclust MeShClust: an intelligent tool for clustering DNA sequences. 1.3 (gcc/8.1.0)
MetaBAT MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities. meso-1.0 (gcc/8.1.0), 0.32.4, 2.12.1
metafast MetaFast is a toolkit for calculating a number of statistics of metagenome sequences and building the distance matrix between them. 0.1.2
methylpy methylpy, python-based WGBS/NOMe-seq Data Processing & Differential Methylation Analysis 1.4.6 (python/3.7.1, gcc/8.1.0)
metis METIS: Serial Graph Partitioning and Fill-reducing Matrix Ordering 5.1.0 (gcc/4.8.4)
microbiomeutil utilities developed by the Broad Institute for a range of challenges posed by the microbiome initiative (NAST-iEr, ChimeraSlayer, TreeChopper, AMOScmp, WigeoN). r20110519 (gcc/4.8.4)
minimap2 minimap2, a versatile pairwise aligner for genomic and spliced nucleotide sequences. 2.17, 2.24
MIRA MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). 4.9.6
mkl Intel Math Kernel Library, a computing math library of highly optimized, extensively threaded routines (BLAS, LAPACK). 2018.1 (intel/2018.1)
MMseqs2 MMseqs2 is an ultra fast and sensitive search and clustering suite. 10-6d92c, 13-45111
mothur Mothur seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. 1.36.1, 1.39.5
MultiQC MultiQC : Aggregate bioinformatics results across many samples into a single report 1.7 (gcc/8.1.0)
MUMmer MUMmer is a versatil alignment tool for DNA and protein sequences. 3.23 (gcc/4.8.4), 4.0.0.beta2 (gcc/8.1.0)
mumps MUMPS: MUltifrontal Massively Parallel sparse direct Solver 5.0.1 (gcc/4.8.4, openmpi/1.8.4)
muparser muParser is an extensible high performance math expression parser library written in C++. 2.2.5 (gcc/4.8.4)
muscle MUSCLE is a multiple alignment program. 3.8.31
ncbi-blast BLAST+: new suite of BLAST tools that utilizes the NCBI C++ Toolkit. 2.2.30+, 2.11.0+
ncl_ncarg The NCAR Command Language (NCL), a product of the Computational & Information Systems Laboratory at the National Center for Atmospheric Research (NCAR) and sponsored by the National Science Foundation, is a free interpreted language designed specifically for scientific data processing and visualization. 6.3.0, 6.6.2
netcdf-c NetCDF-C is a set of C-language software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. 4.4.1.1 (gcc/4.8.4), 4.4.1.1 (gcc/8.1.0)
netcdf-f NetCDF-F is a set of Fortran-language software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. 4.4.4 (gcc/4.8.4), 4.4.4 (gcc/8.1.0)
nextflow Nextflow, Data-driven computational pipelines. 20.04.1
ngsplot Quick mining and visualization of NGS data by integrating genomic databases 2.63
nlopt NLopt is a library for nonlinear local and global optimization, for functions with and without gradient information. 2.5.0 (gcc/4.8.4)
numba Numba: on-the-fly code generation for Python (at import time or runtime, at the user’s preference) 0.22.1 (gcc/4.8.4, python/3.4.5), 0.22.1 (gcc/4.8.4)
numpy Numpy: Module for numerical computation in python (using OpenBLAS) 1.9.2 (gcc/4.8.4, python/3.4.5), 1.9.2 (gcc/4.8.4), 1.18.1 (python/3.7.1, gcc/8.1.0)
openblas OpenBLAS: optimised and multi-threaded BLAS & LAPACK library 0.2.14 (gcc/4.8.4), 0.3.3 (gcc/8.1.0)
openbugs OpenBUGS: Software for performing Bayesian inference Using Gibbs Sampling (MCMC) 3.2.3 (gcc/4.8.4)
opencv OpenCV, open source computer vision and machine learning software library. 3.4.9 (gcc/8.1.0)
openmpi OpenMPI: MPI for C / C++ / Fortran 1.8.4 (intel/2018.1), 1.8.4 (gcc/4.8.4), 3.0.0 (gcc/8.1.0), 3.0.0 (intel/2018.1), 4.0.1 (gcc/8.1.0)
openturns OpenTURNS is a scientific C++ and Python library including an internal data model and algorithms dedicated to the treatment of uncertainties. 1.5 (gcc/4.8.4), 1.8 (gcc/4.8.4)
pandas pandas: Python module providing high-performance, easy-to-use data structures and data analysis tools 0.17.1 (gcc/4.8.4), 0.17.1 (gcc/4.8.4, python/3.4.5), 0.20.3 (gcc/4.8.4), 1.2.4 (python/3.7.1, gcc/8.1.0)
pandaseq PANDAseq: a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. 2.8.1 (gcc/4.8.4)
parallel GNU Parallel: a shell tool for executing jobs in parallel using one or more computers. 20151222
parasail parasail, Pairwise Sequence Alignment 2.4.2 (gcc/8.1.0)
parmetis ParMETIS: Parallel Graph Partitioning and Fill-reducing Matrix Ordering 4.0.3 (gcc/4.8.4, openmpi/1.8.4)
pBWA pBWA : Parallel implementation of BWA using the OpenMPI library. 1.21009 (gcc/8.1.0), 1.21009 (gcc/4.8.4)
PEAR PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. 0.9.11
perl-list-utilsby List::UtilsBy: higher-order list utility functions in Perl 0.11
perl-statistics-r Statistics::R: a Perl module to controls the R interpreter 0.34 (gcc/4.8.4)
phyml PhyML: estimation of maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences 3.3.20170530 (gcc/4.8.4, openmpi/1.8.4)
picard Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. 2.18.25
pindel Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. 0.2.5b8 (gcc/8.1.0)
PIPITS PIPITS is an automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform. 1.5.0 (gcc/4.8.4)
platanus_allee Platanus-allee is a de novo haplotype assembler (phasing tool), which assembles each haplotype sequence in a diploid genome. 2.2.2
ply PLY: Python Lex & Yacc 3.8 (gcc/4.8.4), 3.8 (gcc/4.8.4, python/3.4.5)
price PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. 1.2 (gcc/4.8.4)
prinseq-lite PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data. 0.20.4
prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. 2.6.3
proj PROJ is a generic coordinate transformation software 5.2.0 (gcc/8.1.0)
pstl Parallel STL is an implementation of the C++ standard library algorithms that offers efficient support for both parallel and vectorized execution of algorithms for Intel® processors.. 2018.1 (intel/2018.1)
purge_dups purge haplotigs and overlaps in an assembly based on read depth 1.0.1 (python/3.7.1, gcc/8.1.0), 1.2.5 (python/3.7.1, gcc/8.1.0)
pysam a python module for reading, manipulating and writing genomic data sets. 0.10.0 (gcc/4.8.4), 0.15.3 (python/3.7.1, gcc/8.1.0), 0.15.3 (gcc/8.1.0)
python This module loads the environment for Python 3.4.5. 3.4.5 (gcc/4.8.4), 3.7.1 (gcc/8.1.0), 3.10.10 (gcc/10.2.0), 3.10.10 (gcc/8.1.0), 2.7.9
qhull Qhull: Convex Hull, Delaunay Triangulation, Voronoi Diagram, and Halfspace Intersection about a Point 2012.1 (gcc/4.8.4)
qiime QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. 1.9.1 (gcc/4.8.4)
qt4 Qt4 is a cross-platform application framework. 4.8.7 (gcc/4.8.4)
qt5 Qt5 is a cross-platform application framework. 5.10.1 (gcc/8.1.0), 5.10.1 (gcc/4.8.4)
qualimap Qualimap 2 is a platform-independent application to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. 2.2.2d-2
R R: a free software environment for statistical computing and graphics 3.2.2 (gcc/4.8.4), 3.5.1 (gcc/8.1.0), 3.6.2 (gcc/8.1.0), 4.0.2 (gcc/8.1.0)
RaGOO RaGOO, Fast Reference-Guided Scaffolding of Genome Assembly Contigs 1.11 (python/3.7.1, gcc/8.1.0)
raxml A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. 7.3.0 (gcc/4.8.4)
ray Ray: parallel genome assemblies for parallel DNA sequencing 2.3.1 (gcc/4.8.4, openmpi/1.8.4)
rclone Rclone is a command line program to sync files and directories to and from several storage providers. 1.37, 1.55.1
rdp_classifier rdp_classifier 2.2
RDPTools Metaproject for RDP Tools. 2.0.2
reago an assembly tool for 16S ribosomal RNA recovery from metagenomic data 1.1
Rextra : Collection of R/4.0.2 libraries (abind/1.4-5 ade4/1.7-16 annotate/1.60.1 AnnotationDbi/1.44.0 ape/5.5 assertthat/0.2.1 Biobase/2.42.0 BiocGenerics/0.28.0 BiocParallel/1.16.6 Biostrings/2.50.2 bit/4.0.4 bit64/4.0.5 bitops/1.0-7 blob/1.2.1 broom/0.7.6 BSgenome/1.50.0 bslib/0.2.4 cachem/1.0.4 car/3.0-10 carData/3.0-4 caTools/1.18.2 cellranger/1.1.0 checkmate/2.0.0 circlize/0.4.12 classInt/0.4-3 cli/2.5.0 colorspace/2.0-0 conquer/1.0.2 corrplot/0.84 cowplot/1.1.1 cpp11/0.2.7 crayon/1.4.1 data.table/1.14.0 DelayedArray/0.8.0 dendextend/1.14.0 DESeq2/1.22.2 digest/0.6.27 doMC/1.3.7 dplyr/1.0.5 e1071/1.7-6 ellipse/0.4.2 factoextra/1.0.7 FactoMineR/2.4 fansi/0.4.2 farver/2.1.0 fastmap/1.1.0 fastmatch/1.1-0 flashClust/1.01-2 forcats/0.5.1 foreach/1.5.1 formatR/1.9 Formula/1.2-4 futile.logger/1.4.3 futile.options/1.0.1 gdata/2.18.0 genefilter/1.64.0 geneplotter/1.60.0 generics/0.1.0 GenomeInfoDb/1.18.2 GenomeInfoDbData/1.2.0 GenomicAlignments/1.18.1 GenomicRanges/1.34.0 getopt/1.20.3 ggplot2/3.3.3 ggpubr/0.4.0 ggrepel/0.9.1 ggsci/2.9 ggsignif/0.6.1 GlobalOptions/0.1.2 glue/1.4.2 gplots/3.1.1 gridExtra/2.3 gsalib/2.1 gtable/0.3.0 gtools/3.8.2 haven/2.4.1 Hmisc/4.5-0 HMM/1.0 hms/1.0.0 htmlTable/2.1.0 htmltools/0.5.1.1 httpuv/1.6.0 huge/1.3.4.1 hwriter/1.3.2 igraph/1.2.6 IRanges/2.16.0 isoband/0.2.4 iterators/1.0.13 jpeg/0.1-8.1 jquerylib/0.1.4 labeling/0.4.2 lambda.r/1.2.4 latticeExtra/0.6-29 lazyeval/0.2.2 leaps/3.1 lifecycle/1.0.0 lme4/1.1-26 locfit/1.5-9.4 magrittr/2.0.1 manipulateWidget/0.10.1 maptools/1.1-1 MatrixModels/0.5-0 matrixStats/0.58.0 miniUI/0.1.1.1 minqa/1.2.4 munsell/0.5.0 nloptr/1.2.2.2 numDeriv/2016.8-1.1 openxlsx/4.2.3 optparse/1.6.6 pbkrtest/0.5.1 permute/0.9-5 phangorn/2.6.3 pillar/1.6.0 pixmap/0.4-12 pkgconfig/2.0.3 plogr/0.2.0 plyr/1.8.6 png/0.1-7 polynom/1.4-0 progress/1.2.2 proxy/0.4-25 pulsar/0.3.7 quadprog/1.5-8 quantreg/5.85 R.methodsS3/1.8.1 R.oo/1.24.0 R.utils/2.10.1 R6/2.5.0 rappdirs/0.3.3 RColorBrewer/1.1-2 Rcpp/1.0.6 RcppArmadillo/0.10.4.0.0 RcppEigen/0.3.3.9.1 RCurl/1.98-1.3 readr/1.4.0 readxl/1.3.1 rematch/1.0.1 reshape/0.8.8 reshape2/1.4.4 rgl/0.106.8 rio/0.5.26 rlang/0.4.10 Rsamtools/1.34.1 RSpectra/0.16-0 RSQLite/2.2.7 rstatix/0.7.0 rtracklayer/1.42.2 S4Vectors/0.20.1 sass/0.3.1 scales/1.1.1 scatterplot3d/0.3-41 shape/1.4.5 shiny/1.6.0 ShortRead/1.40.0 snow/0.4-3 sourcetools/0.1.7 sp/1.4-5 SparseM/1.81 statmod/1.4.35 stringi/1.5.3 stringr/1.4.0 SummarizedExperiment/1.12.0 tibble/3.1.1 tidyr/1.1.3 tidyselect/1.1.0 units/0.7-1 utf8/1.2.1 vctrs/0.3.7 vegan/2.5-7 VGAM/1.1-5 viridis/0.6.0 viridisLite/0.4.0 webshot/0.5.2 wordcloud/2.6 XML/3.99-0.6 xtable/1.8-4 XVector/0.22.0 zip/2.1.1 zlibbioc/1.28.0 Biobase/2.46.0 BiocGenerics/0.32.0 BiocVersion/3.10.1 coda/0.19-3 deldir/0.1-25 expm/0.999-4 gam/1.16.1 ggplotify/0.0.5 gmodels/2.18.1 gridGraphics/0.5-1 inline/0.3.15 LearnBayes/2.15.1 lpSolve/5.6.15 NOISeq/2.30.0 raster/3.0-12 RcppGSL/0.3.6 rvcheck/0.1.8 spData/0.3.5 spdep/1.1-3 sphet/1.7 askpass/1.1 assertthat/0.2.1 backports/1.1.9 base64enc/0.1-3 BH/1.72.0-3 brew/1.0-6 callr/3.4.3 cli/2.0.2 clipr/0.7.0 commonmark/1.7 covr/3.5.0 crayon/1.3.4 crosstalk/1.1.0.1 curl/4.3 DBI/1.1.0 desc/1.2.0 devtools/2.3.1 digest/0.6.25 DT/0.15 ellipsis/0.3.1 evaluate/0.14 fansi/0.4.1 fs/1.5.0 gh/1.1.0 git2r/0.27.1 glue/1.4.2 highr/0.8 htmltools/0.5.0 htmlwidgets/1.5.1 httr/1.4.2 ini/0.3.1 jsonlite/1.7.0 knitr/1.29 later/1.1.0.1 lazyeval/0.2.2 lifecycle/0.2.0 magrittr/1.5 markdown/1.1 memoise/1.1.0 mime/0.9 openssl/1.4.2 pillar/1.4.6 pkgbuild/1.1.0 pkgconfig/2.0.3 pkgload/1.1.0 praise/1.0.0 prettyunits/1.1.1 processx/3.4.3 promises/1.1.1 ps/1.3.4 purrr/0.3.4 R6/2.4.1 rcmdcheck/1.3.3 Rcpp/1.0.5 rematch2/2.1.2 remotes/2.2.0 rex/1.2.0 rlang/0.4.7 roxygen2/7.1.1 rprojroot/1.3-2 rstudioapi/0.11 rversions/2.0.2 sessioninfo/1.1.1 stringi/1.4.6 stringr/1.4.0 sys/3.4 testthat/2.3.2 tibble/3.0.3 usethis/1.6.1 utf8/1.1.4 vctrs/0.3.4 whisker/0.4 withr/2.2.0 xfun/0.16 xml2/1.3.2 xopen/1.0.0 yaml/2.2.1) 0.1 (gcc/8.1.0), 10.0 (gcc/8.1.0)
rgl : rgl: high level functions for 3D interactive graphics 0.96.0 (gcc/4.8.4)
rocksdb RocksDB : A Persistent Key-Value Store for Flash and RAM Storage 5.17.2 (gcc/8.1.0)
root Root: Big data processing, statistical analysis, visualisation and storage 5.34.36, 6.14.06 (gcc/8.1.0), 6.28.04 (gcc/10.2.0)
RSEM RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. 1.3.1 (gcc/8.1.0)
rtax Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene. 0.984
RTK open-source and cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit (ITK) 1.4.0 (gcc/4.8.4)
ruby Ruby language. 2.4.2 (gcc/8.1.0), 2.4.2 (gcc/4.8.4)
s3cmd Command line tool for managing S3 services 2.0.1 (gcc/4.8.4)
s3fs s3fs allows Linux to mount an S3 bucket via FUSE. 1.82 (gcc/4.8.4)
s5cmd s5cmd is a very fast S3 and local filesystem execution tool. 2.2.2
salmon Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. 0.12.0 (gcc/8.1.0)
samtools Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format 1.3 (gcc/4.8.4), 1.9 (gcc/8.1.0), 1.16.1 (gcc/8.1.0)
scalapack ScaLAPACK: Library of high-performance linear algebra routines for parallel distributed memory machines 2.0.2 (gcc/4.8.4, openmpi/1.8.4)
scipy SciPy: Scientific Library for Python 0.15.1 (gcc/4.8.4), 0.15.1 (gcc/4.8.4, python/3.4.5)
seqkit SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation 0.15.0
seqmagick Seqmagick is a kickass little utility built in the spirit of imagemagick to expose the file format conversion in Biopython in a convenient way. 0.6.2 (gcc/4.8.4)
SeqPrep Tool for stripping adaptors and/or merging paired reads with overlap into single reads. 1.1 (gcc/4.8.4)
SeqPrep2 Tool for stripping adaptors and/or merging paired reads with overlap into single reads. 1.1 (gcc/8.1.0), 1.1-93fccac (gcc/8.1.0)
settarg The settarg module provides a way to connect the loaded modules with your build system by setting environment variables.
(no specific version)
SICER Recognizes ChIP-enriched regions in histone modification data. 1.1 (gcc/4.8.4)
signalp SignalP, Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences. 5.0b
smrttools smrttools, Tools from SMRT Link. These tools are for use by bioinformaticians working with secondary analysis results. 10.2.0.133434, 11.0.0.146107, 12.0.0.177059
snakemake The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. 5.6.0 (python/3.7.1, gcc/8.1.0), 5.25.0 (python/3.7.1, gcc/8.1.0), 7.15.1 (python/3.7.1, gcc/8.1.0)
snpeff SnpEff, Genomic variant annotations and functional effect prediction toolbox. 4.3t
SOAPdenovo2 SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. 2.4.1
SortMeRNA next-generation sequence filtering and alignment tool. 2.0 (gcc/4.8.4), 3.0.2 (gcc/8.1.0), 4.2.0 (gcc/8.1.0)
SPAdes SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. 3.10.1, 3.15.0
sparsehash sparsehash, C++ associative containers 2.0.3 (gcc/8.1.0)
SQANTI3 SQANTI3, extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification 1.6
sratoolkit The SRA Toolkit from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. 2.9.0, 3.0.0
STAR Spliced Transcripts Alignment to a Reference - RNA-seq aligner. 2.6.1 (gcc/8.1.0), 2.7.2b (gcc/8.1.0), 2.7.3a (gcc/8.1.0), 2.7.7a (gcc/8.1.0)
stringtie stringtie, Transcript assembly and quantification for RNA-Seq 2.0.3
subread The Subread package, a tool kit for processing next-gen sequencing data. 2.0.1 (gcc/8.1.0)
sumaclust Fast and exact comparison and clustering of sequences. 1.0.00 (gcc/4.8.4)
swarm A robust and fast clustering method for amplicon-based studies. 1.2.19 (gcc/4.8.4)
swig SWIG - Simplified Wrapper and Interface Generator. 3.0.12 (gcc/4.8.4)
t-coffee T-Coffee is a multiple sequence alignment package. 12.00.142ba30
tabix tabix, Generic indexer for TAB-delimited genome position files 0.2.6
targetp TargetP, Subcellular location of proteins: mitochondrial, chloroplastic, secretory pathway, or other. 2.0
tbb Widely used C++ template library for task parallelism. 2017.3 (gcc/4.8.4), 2018.1 (intel/2018.1), 2019.3 (gcc/8.1.0)
tensorflow TensorFlow is an open source software library for numerical computation using data flow graphs. 1.8.0 (gcc/4.8.4, python/3.4.5)
TestU01 A Software Library in ANSI C for Empirical Testing of Random Number Generators. 1.2.3 (gcc/4.8.4)
TopHat TopHat is a fast splice junction mapper for RNA-Seq reads. 2.1.1
TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. 5.5.0
trf TRF (Tandem Repeats Finder) locate and display tandem repeats in DNA sequences 4.0.4
TrimGalore 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. 0.5.0, 0.6.5
trimmomatic Trimmomatic, a flexible read trimming tool for Illumina NGS data. 0.33, 0.38
trimmotatic Trimmomatic, a flexible read trimming tool for Illumina NGS data. 0.36
trinityrnaseq Trinity assembles transcript sequences from Illumina RNA-Seq data. 2.2.0 (gcc/4.8.4), 2.8.4 (gcc/8.1.0), 2.9.1 (gcc/8.1.0), 2.13.2 (gcc/8.1.0)
ucsc-tools ucsc-tools 1.0
uproot Uproot is a reader and a writer of the ROOT file format using only Python and Numpy. 4.0.7 (python/3.7.1, gcc/8.1.0)
usearch USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST. 7.0.1090, 9.2.64
varscan varscan, Variant calling and somatic mutation/CNV detection for next-generation sequencing data 2.4.2
vcftools VCFtools, A set of tools written in Perl and C++ for working with VCF files 0.1.16 (gcc/8.1.0)
vsearch The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010). 2.3.4 (gcc/4.8.4), 2.4.4 (gcc/4.8.4)
yak yak, robustly estimates the base accuracy of CCS reads and assembly contigs, investigates the systematic error rate of CCS reads. 0.1-r56 (gcc/8.1.0)
zinba : Zero Inflated Negative Binomial Algorithm 2.02.03 (gcc/4.8.4)