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List of modules available on ACCRE

This page contains a list of modules available on Lmod, including modules available on the GPU accelerated nodes. This list is updated at the start of each month.

If you cannot find a package you would like to use below, please open a helpdesk ticket with us and we can either help you install it into your home directory, or possibly install it for cluster-wide access.

List of modules available on regular compute nodes

Last updated May 5, 2020
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.
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
19.0.01 (Py2)
AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
Amber17 (Py2)Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Amber 16 patch 15 + AmberTools 17 patch 10
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.
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.
2.3.0 (Py2)
ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.
Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
Aspera-CLI3.7.7IBM 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.
3.3.2 (Py2)
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
Bazel0.10.0Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
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.
BerkeleyGW2.0.0The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.
Bio-DB-HTS2.11Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
biomart-perl0.7_e6db561The BioMart Perl API allows you to go a step further with BioMart and integrate BioMart Perl Code into custom Perl scripts.
BioPerl1.7.1Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.
Biopython1.68 (Py2)
1.68 (Py3)
1.70 (Py2)
1.70 (Py3)
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
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.
Boost1.63.0 (Py2)
1.63.0 (Py3)
1.65.1 (Py2)
1.65.1 (Py3)
Boost provides free peer-reviewed portable C++ source libraries.
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
BWA0.7.17Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
canu1.8Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing
Copy number variant (CNV) calling from DNA sequencing data
Cartopy0.17Cartopy is a Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses.
CellRanger3.0.0Cell 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.
CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems.
CheckM1.0.13 (Py2)
1.0.13 (Py3)
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
ciftify2.3.2.post1 (Py3)
2.3.2.post1 (Py3)
The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
CLAPACK3.2.1C version of LAPACK
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
CNVnator8302019a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads.
COMSOL5.4COMSOL Multiphysics - Simulation Tool for Electrical, Mechanical, Fluid Flow, and Chemical Applications
CONCOCT1.0.0 (Py2)
1.0.0 (Py3)
Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
ConnectomeWorkbench1.3.2Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.
cutadapt1.9.1 (Py2)
1.9.1 (Py3)
1.16 (Py2)
1.16 (Py3)
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Cython0.29.10 (Py2)
0.29.10 (Py3)
The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.
DBD-mysql4.046Perl binding for MySQL
DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies
dcm2niix is a designed program to convert neuroimaging data from the DICOM format to the NIfTI format.
Delly0.7.8Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.
ds3_python3_sdk4.1.0 (Py3)An SDK conforming to the Spectra S3 specification for Python 3.6
duphold0.2.1SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content.
Eigen3.3.7Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
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.
Exonerate2.4.0Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
A complete, cross-platform solution to record, convert and stream audio and video.
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.
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging.
6.0.1 (Py2)
6.0.1 (Py3)
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
0.18.2 (Py2)
FSLeyes is the FSL image viewer.
garfieldpp2017.2 (Py2)Garfield++ is a toolkit for the detailed simulation of particle detectors that use gas and semi-conductors as sensitive medium. The main area of application is currently in micropattern gaseous detectors.
8.2 (Py2)
GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography
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.
Gaussian16.B.01Gaussian provides state-of-the-art capabilities for electronic structure modeling.
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,...).
2.2.3 (Py2)
3.0.0 (Py2)
3.0.0 (Py3)
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 commandline utilities for data translation and processing.
8.0.1 (Py2)
8.0.1 (Py3)
The GNU Project Debugger
Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
GenomeSTRiP2.00.1918Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals. Genome STRiP looks both across and within a set of sequenced genomes to detect variation. The methods are adaptive and support heterogeneous data sets, including variations in sequencing depth, read lengths and mixtures of paired and single-end reads. A minimum of 20 to 30 genomes are required to get acceptable results, but the method gains power across genomes and processing more genomes provide better results.
git-lfs2.7.1Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like
Portable interactive, function plotting utility
Go1.12Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
grace5.1.25Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.
GraphicsMagick is the swiss army knife of image processing.
Graphviz2.38.0 (Py2)
2.40.1 (Py2)
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.
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.
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.
h5py2.6.0 (Py2)
2.6.0 (Py3)
2.7.1 (Py2)
2.7.1 (Py3)
HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
Hadoop2.7.7The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.
Harminv1.4.1Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
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).
HTSeq0.9.1 (Py2)
0.9.1 (Py2)
0.9.1 (Py3)
A framework to process and analyze data from high-throughput sequencing (HTS) assays is a collaborative initiative funded by the National Institutes of Neurological Disorders and Stroke. This initiative seeks to advance research towards the understanding of epilepsy by providing a platform for sharing data, tools and expertise between researchers. This MATLAB toolbox makes getting data into MATLAB, and uploading annotations to the portal simple.
ieeg-cli1.14.56IEEG.ORG is a collaborative initiative funded by the National Institutes of Neurological Disorders and Stroke. This initiative seeks to advance research towards the understanding of epilepsy by providing a platform for sharing data, tools and expertise between researchers.
ImageMagick is a software suite to create, edit, compose, or convert bitmap images
IMPUTE22.3.2IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009
Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
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.
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 3.0 (MPI-3) specification.
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.
IPython5.8.0 (Py2)
5.8.0 (Py3)
7.7.0 (Py3)
IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.
IRkernel0.8.15 (Py2)The R kernel for the 'Jupyter' environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.
ITK4.12.2 (Py2)
5.0.1 (Py3)
Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data.
ITK-SNAP3.8.0ITK-SNAP is a software application used to segment structures in 3D medical images, and it provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation.
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
Julia1.4.0Julia is a high-level, high-performance dynamic programming language for numerical computing
LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind.
libctl4.1.4libctl is a free Guile-based library implementing flexible control files for scientific simulations.
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.
LoFreq2.1.3.1 (Py2)Fast and sensitive variant calling from next-gen sequencing data
Lua5.2.4Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
LUMPY0.3.0A probabilistic framework for structural variant discovery.
MACS22.1.1.20160309 (Py2) (Py2)
Model Based Analysis for ChIP-Seq data
manta1.6.0Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.
MariaDB10.2.11MariaDB An enhanced, drop-in replacement for MySQL.
matchclips204-09-2014This is an updated version of matchclips to precisely locate the break points of structure variations. This update mainly focuses on speed and reproducibility, and is intended for real data large files. A 70x coverage whole genome sequencing BAM file should take about 5-8 hours on a single cpu and use about 2-3GB memory. It is not really helpful to use more than 4 cores. Performance suffers if the computing node is disk IO busy.
Mathematica12.0.0Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.
MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
MATLAB-Engine2018b (Py2)
2018b (Py3)
The MATLAB Engine API for Python provides a package for Python to call MATLAB as a computational engine.
matplotlib1.5.3 (Py2)
1.5.3 (Py3)
2.1.0 (Py2)
2.1.0 (Py3)
2.2.4 (Py2)
3.0.3 (Py3)
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.
MCRR2016aThe MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
MEGAHIT1.1.3 (Py2)
1.1.3 (Py3)
An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
5.0.4 (Py2)
5.0.4 (Py3)
The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.
Metal2011-03-25Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.
METIS5.1.0METIS 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.
An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
mosdepth0.2.6fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
MPB1.7.0MPB is a free and open-source software package for computing electromagnetic band structures and modes.
mpi4py1.3.1 (Py2)
1.3.1 (Py2)
1.3.1 (Py3)
1.3.1 (Py3)
MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
MRIcron1.0.20180614MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering.
Multimodal Surface Matching with Higher order Clique Reduction
MultiQC1.2 (Py2)
1.2 (Py3)
1.6 (Py2)
1.6 (Py3)
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.
MUSCLE3.8.31MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks.
MySQL is one of the world's most widely used open-source relational database management system (RDBMS).
NAMD2.12NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Net-core2.1.8.NET Core is a free and open-source managed computer software framework for the Windows, Linux, and macOS operating systems .NET Core fully supports C# and F# and partially supports Visual Basic
Nextflow19.04.0Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data
NiBabel2.1.0 (Py2)
2.3.0 (Py2)
2.3.0 (Py3)
NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.
Nilearn0.5.2 (Py2)
0.5.2 (Py3)
Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.
numpy1.11.1 (Py2)
1.11.1 (Py3)
1.13.1 (Py2)
1.13.1 (Py3)
NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.
GNU Octave is a high-level interpreted language, primarily intended for numerical computations.
octave_kernel0.28.4 (Py2)
0.28.4 (Py3)
Octave kernel for IPython Notebook
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
3.3.0 (Py2)
3.3.0 (Py3)
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.
The Open MPI Project is an open source MPI-2 implementation.
p7zip16.02p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
pandas0.18.1 (Py2)
0.18.1 (Py2)
0.18.1 (Py3)
0.18.1 (Py3)
0.20.1 (Py2)
pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.
PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
ParaView is a scientific parallel visualizer.
ParMETIS4.0.3ParMETIS 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.
PEAR0.9.10PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.
Larry Wall's Practical Extraction and Report Language
PGI18.1C, C++ and Fortran compilers from The Portland Group - PGI
PHAST is a freely available software package for comparative and evolutionary genomics.
Provides an accessible R interface to the phenome wide association study.
PHYLIP is a free package of programs for inferring phylogenies.
A set of tools (in Java) for working with next generation sequencing data in the BAM format.
Pindel0.2.5b9-20170508Pindel 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. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
plink-1.9-x86_64: Whole-genome association analysis toolset
PLINKSEQ0.1PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
PLUMED2.5.2 (Py3)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.
PostgreSQL9.6.2 (Py2)
10.3 (Py2)
PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.
The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports.
pplacer1.1.alpha19Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
pplpy0.8.4 (Py2)
0.8.4 (Py3)
This Python package provides a wrapper to the C++ Parma Polyhedra Library (PPL).
prodigal2.6.3Prodigal (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.
Pysam0.10.0 (Py2)
0.14 (Py2)
0.14 (Py3)
0.15.2 (Py2)
0.15.2 (Py3)
Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
Python is a programming language that lets you work more quickly and integrate your systems more effectively.
Qhull2015.2Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.
QIIME1.9.1QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
QIIME22019.4QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
qrupdate1.1.2qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.
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).
R is a free software environment for statistical computing and graphics.
R is a free software environment for statistical computing and graphics.
RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
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).
RepeatMasker4.0.8RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
RERconverge0.1.0RERconverge is a set of software written in R that estimates the correlation between relative evolutionary rates of genes and the evolution of a convergent binary or continuous trait across a phylogeny.
ROOT6.10.02 (Py2)
6.10.08 (Py2)
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.
RNA-Seq by Expectation-Maximization
RStan2.18.2RStan is the R interface to Stan. Stan is a state-of-the-art platform for statistical modeling and high-performance statistical computation.
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.
s3cmd2.0.2 (Py3)S3cmd is a free command line tool and client for uploading, retrieving and managing data in Amazon S3 and other cloud storage service providers that use the S3 protocol, such as Google Cloud Storage or DreamHost DreamObjects. It is best suited for power users who are familiar with command line programs. It is also ideal for batch scripts and automated backup to S3, triggered from cron, etc.
S41.1.1S4 stands for Stanford Stratified Structure Solver, a frequency domain code to solve the linear Maxwell’s equations in layered periodic structures. Internally, it uses Rigorous Coupled Wave Analysis (RCWA, also called the Fourier Modal Method (FMM)) and the S-matrix algorithm.
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
SAS9.4SAS is a software suite for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.
ScaLAPACK2.0.2The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
scikit-learn0.19.1 (Py2)
0.19.1 (Py3)
Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.
scilo-gui5.0.4Eon Browser provides users an easy-to-use tool to archive files to the BlackPearl Deep Storage Gateway.
scipy0.17.0 (Py2)
0.17.0 (Py3)
0.19.1 (Py2)
0.19.1 (Py3)
SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python.
SciPy-bundle2019.03Bundle of Python packages for scientific software
Seaborn0.9.0 (Py2)
0.9.0 (Py2)
0.9.0 (Py3)
0.9.0 (Py3)
Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.
SimpleElastix0.10.0 (Py3)Multi-lingual medical image registration library.
smoove0.2.4smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls.
SNAP2013-11-29SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.
SNPhylo20160204 (Py2)
SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo.
Spark is Hadoop MapReduce done in memory
SQLite: SQL Database Engine in a C Library
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
STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.
statsmodels0.9.0 (Py2)Statsmodels is a Python package that provides a complement to scipy for statistical computations including descriptive statistics and estimation and inference for statistical models.
Subversion is an open source version control system.
SuiteSparse is a collection of libraries manipulate sparse matrices.
survivor1.0.6SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.
SVDetect0.8bSVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identifying structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale.
svtools0.5.1 (Py2)svtools is a suite of utilities designed to help bioinformaticians construct and explore cohort-level structural variation calls. It is designed to efficiently merge and genotype calls from speedseq sv across thousands to tens of thousands of genomes.
svtyper0.7.1 (Py2)Bayesian genotyper for structural variants
3.0.12 (Py2)
SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
tabix0.2.6Generic indexer for TAB-delimited genome position files
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.
TensorFlow1.8.0 (Py2)
1.8.0 (Py3)
An open-source software library for Machine Intelligence
tesseract4.1.0Tesseract is an optical character recognition engine
TopHat2.1.1 (Py2)TopHat is a fast splice junction mapper for RNA-Seq reads.
TRF4.09Tandem repeats finder: a program to analyze DNA sequences. Legacy version.
UMI-tools1.0.0 (Py3)UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
V82.3R interface to Google's open source JavaScript engine
Valgrind: Debugging and profiling tools
A set of tools written in Perl and C++ for working with VCF files.
VEP94.5Variant 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.
Wannier902.1.0A tool for obtaining maximally-localised Wannier functions
XTandem17.02.01.4X!Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification.

List of modules available on GPU nodes

Last updated May 5, 2020.
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.
The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
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 builds.
Keras2.2.0 (Py2)
2.2.0 (Py3)
Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.
magma2.3.0The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.
Meep1.6.0 (Py2)Meep (or MEEP) is a free finite-difference ain (FDTD) simulation software package developed at MIT to model electro systems.
PyTorch0.3.1 (Py2)
0.3.1 (Py3)
Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.
Theano1.0.2 (Py2)
1.0.2 (Py3)
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.