## **Biology category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
ARAGORN|detects tRNA and tmRNA genes.|1.2.38-foss-2019b
AUGUSTUS|Augustus predicts genes in eukaryotic genomic sequences.|3.3.3-foss-2019b
BamTools|BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files|2.5.1-intel-2019b 2.5.1-GCC-8.3.0
BCFtools|BCFtools are a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart, BCF|1.10.2-intel-2019b 1.10.2-GCC-8.3.0
BEDTools|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.|2.28.0-intel-2019b
BioPerl|Bioperl 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.|1.7.2-GCCcore-8.3.0
BLASR|BLASR (Basic Local Alignment with Successive Refinement) is used for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error.|5.3.3-gompi-2019b
BLAST+|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.|2.10.0-gompi-2019b
BLASTDB|BLAST search pages under the Basic BLAST section of the NCBI BLAST home page (https://blast.ncbi.nlm.nih.gov/) use a standard set of BLAST databases for nucleotide, protein, and translated BLAST searches.|v5
Bowtie|Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.|1.2.3-GCC-8.3.0
Bowtie2|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.|2.3.5.1-GCC-8.3.0
BWA|Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.|0.7.17-intel-2019b
canu|Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).|1.9-GCCcore-8.3.0-Java-11
DIAMOND|Diamond is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity.|0.9.32-GCC-8.3.0
FastQC|FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.|0.11.9-Java-11
GATK|The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV).|4.1.4.1-GCCcore-8.3.0-Java-11 3.8-Java-1.8.0_241
GMAP-GSNAP|GMAP is a tools for rapidly and accurately mapping and aligning cDNA sequences to genomic sequences.|2020-04-08-GCC-8.3.0
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. This is a GPU enabled build, containing both MPI and thread MPI binaries.|2019.5-fosscuda-2019b
HISAT2|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).|2.2.0-foss-2019b
HMMER|HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models|3.2.1-gompi-2019b
HTSlib|A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix|1.10.2-GCC-8.3.0
IQ-TREE|Efficient phylogenomic software by maximum likelihood|1.6.12-intel-2019b
Infernal|Infernal (“INFERence of RNA ALignment”) is for searching DNA sequence databases for RNA structure and sequence similarities.|1.1.3-intel-2019b
LAMMPS|LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It’s an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.|3Mar2020-foss-2019b-Python-3.7.4-kokkos
LASTZ|LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by high-throughput sequencing technologies such as Roche 454|1.04.03-foss-2019b
MAFFT|MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate’ for alignment of < ~200 sequences), FFT-NS-2 (fast; for alignment of < ~30000 sequences), etc|7.453-iccifort-2019.5.281-with-extensions
minimap2|Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the SAM format|2.17-GCC-8.3.0
ncbi-vdb|The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.|2.10.0-foss-2019b
NGS|Here we provide a general workflow for NGS data analysis with RNA-Seq, ChIP-Seq and RRBS-Seq (Reduced Representation of bisulfite sequencing, a cost effecient alternative to whole genome bisulfite sequencing).|2.10.0-GCCcore-8.3.0
PHYLIP|PHYLIP is a package for inferring phylogenies.|3.697-GCC-8.3.0
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. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.|2.21.6-Java-11
Pilon|Pilon is a software tool which can be used to automatically improve draft assemblies find variation among strains, including large event detection.|1.23-Java-11
RAxML|Randomized Axelerated Maximum Likelihood based inference of large phylogenetic trees|8.2.12-intel-2019b-hybrid-avx2
Racon|Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies|1.4.13-GCCcore-8.3.0
R-bundle-Bioconductor|This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects|3.10-fosscuda-2019b-R-3.6.2
 Ray|Ray is a parallel de novo genome assembler that utilises the message-passing interface everywhere and is implemented using peer-to-peer communication. Ray is free software distributed under the terms of the GNU General Public License, version 3 (GPLv3). Ray is implemented using RayPlatform, a message-passing-interface programming framework.|2.3.1-iimpi-2019b
RepeatMasker|RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).|4.0.9-p2-gompi-2019b-HMMER
SAMtools|SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.|1.10-GCC-8.3.0 1.9-intel-2019b
SNAP|snap: Semi-HMM-based Nucleic Acid Pars|4.6.0-foss-2019b-Perl-5.30.0
SPAdes|SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads.|3.14.0-GCC-8.3.0
STAR|Spliced Transcripts Alignment to a Reference|2.7.3a-GCC-8.3.0
TRF|Tandem repeats finder: a program to analyze DNA sequences. Legacy version.|4.09-linux64
Trinity|Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data.|2.8.5-GCC-8.3.0-Java-11
VCFtools|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.|0.1.16-GCC-8.3.0
Unicycler|Unicycler is an assembly pipeline for bacterial genomes.|0.4.8-foss-2019b-Python-3.7.4

Biology

## **Chemistry category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
Gaussian|Gaussian is a quantum chemistry program produced by Gaussian, Inc. Since Gaussian is commercially licensed software, only users from an institution that has purchased a license can use Gaussian, or any additionally licensed special features, on that institution’s LONI machine.|16.B.01-AVX2
kim-api|The Knowledgebase of Interatomic Models (KIM) Application Programming Interface (API) defines a standard (the Portable Model Interface (PMI)) for how molecular simulators interface with interatomic models (also called potentials or force-fields).|2.1.3-foss-2019b
ORCA|Some users have requested an installation of the ORCA quantum chemistry program on Stallo.|4.2.1-gompi-2019b
PLUMED|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|2.5.3-foss-2019b-Python-3.7.4
molmod|MolMod is a Python library with many components that are useful to write molecular modeling programs.|1.4.5-foss-2019b-Python-3.7.4
VASP|The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.|5.4.4-vtst-intel-2019b
VASPsol|We have implemented an implicit solvation model that describes the effect of electrostatics, cavitation, and dispersion on the interaction between a solute and solvent into the plane-wave DFT code VASP. Our implementation provides a computationally efficient means to calculate the effects of solvation on molecules and crystal surfaces as well as reaction barriers. The strength of our solvation model implementation is its capability to handle large periodic systems such as metal and semiconductor surfaces and its interoperability with standard ultrasoft pseudopotential and projector-augmented wave potential libraries.|5.4.4-vtst-intel-2019b
yaff|Yaff is created to provide a good reference implementation of the force fields developed at the Center for Molecular Modeling at the Ghent University. In its current version, Yaff is general and flexible enough to handle a large variety of force field models.|1.6.0-foss-2019b-Python-3.7.4

Chemistry

## **Compilers category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
Clang|C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library — use libstdc++ from GCC.|9.0.1-GCC-8.3.0-CUDA-10.1.243
GCC|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,…).|8.3.0
GCCcore|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,…).|8.3.0
PGI|C, C++ and Fortran compilers from The Portland Group – PGI|19.10-GCC-8.3.0-2.32
LLVM|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.|9.0.0-GCCcore-8.3.0

Compilers

## **Data processing category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
HDF5|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.|1.10.5-iimpi-2019b 1.10.5-gompi-2019b 1.10.5-gompic-2019b
h5py|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.|2.10.0-foss-2019b-Python-3.7.4
LAME|LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL|LAME/3.100-GCCcore-8.3.0
ncdf4|Interface to Unidata netCDF (version 4 or earlier) format data files|1.16.1-fosscuda-2019b-R-3.6.2
netCDF|NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.|4.7.1-gompi-2019b 4.7.1-fosscuda-2019b

Data processing

## **Development category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
Automake|Automake: GNU Standards-compliant Makefile generator|1.16.1-GCCcore-8.3.0 1.15.1-GCCcore-8.3.0 
Autoconf|Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.|2.69-GCCcore-8.3.0
Autotools|This bundle collect the standard GNU build tools: Autoconf, Automake and libtool|20180311-GCCcore-8.3.0
CMake|CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.|3.15.3-GCCcore-8.3.0
gperf|GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.|3.1-GCCcore-8.3.0
gtest|Google’s framework for writing C++ tests on a variety of platforms|1.10.0-GCCcore-8.3.0
PCRE|The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.|8.43-GCCcore-8.3.0
PCRE2|The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.|10.33-GCCcore-8.3.0
pkgconfig|pkgconfig is a Python module to interface with the pkg-config command line tool|1.5.1-GCCcore-8.3.0-Python-3.7.4
SQLite|SQLite: SQL Database Engine in a C Library|3.29.0-GCCcore-8.3.0

Development

## **Engineer simulation category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
ANSYS|ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.|19.3
HyperWorks|Altair HyperWorks offers solutions for all engineers ‐ from model-based systems design and early geometry ideation, to detailed multiphysics simulation and optimization. HyperWorks enables simulation driven design, with the physics-based design solutions to deliver the complex products your customers demand.|2019.2

Engineer simulation

## **Libraries category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
ant|Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. Ant supplies a number of built-in tasks allowing to compile, assemble, test and run Java applications.|1.10.7-Java-11
gc|The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.|7.6.12-GCCcore-8.3.0
libmatheval|GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.|1.1.11-GCCcore-8.3.0
libunistring|This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.|0.9.10-GCCcore-8.3.0
LMDB|LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.|0.9.24-GCCcore-8.3.0
NSPR|Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.|4.21-GCCcore-8.3.0  
NSS|Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications|3.45-GCCcore-8.3.0
Tk|Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI not only for Tcl, but for many other dynamic languages, and can produce rich, native applications that run unchanged across Windows, Mac OS X, Linux and more.|8.6.9-GCCcore-8.3.0

Libraries

## **Mathematics category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
GMP|GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.|6.1.2-GCCcore-8.3.0
METIS|METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.|5.1.0-GCCcore-8.3.0 
tbb|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.|2019_U9-GCCcore-8.3.0

Mathematics

## **MPI category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
impi|Intel MPI Library, compatible with MPICH ABI|2018.5.288-iccifort-2019.5.281
OpenMPI|The Open MPI Project is an open source MPI-3 implementation.|3.1.4-gcccuda-2019b 3.1.4-GCC-8.3.0

## **Numerical libraries category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
cuDNN|The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.|7.6.5.32-CUDA-10.1.243 7.6.4.38-CUDA-10.0.130
FFTW|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.|3.3.8-gompic-2019b 3.3.8-gompi-2019b
imkl|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.|2019.5.281-iimpi-2019b
NLopt|NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.|2.6.1-GCCcore-8.3.0
OpenBLAS|OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.|0.3.7-GCC-8.3.0
ScaLAPACK|The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.|2.0.2-gompic-2019b 2.0.2-gompi-2019b
SuiteSparse|A suite of sparce matrix software including UMFPACK, CHOLMOD, SPQR, KLU, BTF, AMD, CAMD, COLAMD, CCOLAMD, a concise sparse Cholesky factorization package, UFget Matlab interface for the UF Sparse Matrix Collection, spqr_rank, factorisation, SSMULT, SFMULT sparse matrix multiplication and other tools.|5.6.0-foss-2019b-METIS-5.1.0

Numerical libraries

## **Physics category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
UDUNITS|UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.|2.2.26-GCCcore-8.3.0
QuantumESPRESSO|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|6.5-intel-2019b

Physics

## **Programming Languages category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
Guile|Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts.|1.8.8-GCCcore-8.3.0
Java|Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers|11.0.2 1.8.0_241
NASM|NASM: General-purpose x86 assembler|2.14.02-GCCcore-8.3.0
Perl|Larry Wall’s Practical Extraction and Report Language|5.30.0-GCCcore-8.3.0
Python|Python is a programming language that lets you work more quickly and integrate your systems more effectively.|3.7.4-GCCcore-8.3.0 2.7.16-GCCcore-8.3.0
R|R is a free software environment for statistical computing and graphics.|3.6.2-fosscuda-2019b
SciPy-bundle|Bundle of Python packages for scientific software|2019.10-foss-2019b-Python-3.7.4
Tcl|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.|8.6.9-GCCcore-8.3.0
Tkinter|Tkinter module, built with the Python buildsystem|3.7.4-GCCcore-8.3.0
Voro++|Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation.|0.4.6-foss-2019b
Yasm|Yasm: Complete rewrite of the NASM assembler with BSD license|1.3.0-GCCcore-8.3.0

Programming Languages

## **System-level software category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
CUDA|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.|10.1.243 10.0.130 10.1.243-GCC-8.3.0

System-level software

## **Toolchains (software stacks) category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
gcccuda|GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.|2019b
gompi|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.|2019b
gompic|GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.|2019b
foss|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK|2019b
fosscuda|GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.|2019b
iccifort|Intel C, C++ & Fortran compilers|2019.5.281
intel|Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).|2019b
iimpi|Intel C/C++ and Fortran compilers, alongside Intel MPI.|2019b

Toolchains (software stacks)

## **Utilities category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
archspec|Archspec aims at providing a standard set of human-understandable labels for various aspects of a system architecture like CPU, network fabrics, etc. and APIs to detect, query and compare them.|0.1.0-GCCcore-8.3.0-Python-3.7.4
binutils|binutils: GNU binary utilities|2.32-GCCcore-8.3.0
bzip2|bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.|1.0.8-GCCcore-8.3.0
cURL|libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.|7.66.0-GCCcore-8.3.0
EasyBuild|EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.|4.2.0
Ghostscript|Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.|9.50-GCCcore-8.3.0
Inspector|Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications|2019_update5
Singularity|Singularity is an open source container platform designed to be simple, fast, and secure. Singularity is optimized for EPC and HPC workloads, allowing untrusted users to run untrusted containers in a trusted way.|3.4.2 3.3.0
VTune|Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.|2019_update5
XZ|XZ utils: General purpose data compression supporting LZMA|5.2.4-GCCcore-8.3.0

Utilities

## **Visualization category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
FFmpeg|A complete, cross-platform solution to record, convert and stream audio and video.|4.2.1-GCCcore-8.3.0
GLib|GLib is one of the base libraries of the GTK+ project|2.62.0-GCCcore-8.3.0
gnuplot|Portable interactive, function plotting utility|5.2.8-GCCcore-8.3.0
ImageMagick|ImageMagick is a software suite to create, edit, compose, or convert bitmap images|7.0.9-5-GCCcore-8.3.0
iVar|IVAR extracts surveillance video insights and delivers actionable suspect and object identification results for law-enforcement and commercial entities. Compatible with industry protocols and standards like ONVIF, RTSP and H.264, this solution integrates into devices with built-in cameras offering value-added applications in different verticals like retail, industrial, banking, education, public safety and provides advanced dataset services for cloud servers.|1.0.1-foss-2019b
matplotlib|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.|3.1.1-foss-2019b-Python-3.7.4
x264|x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.|20190925-GCCcore-8.3.0
x265|x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.|3.2-GCCcore-8.3.0

Visualization

## **Biology category**

| Name| Description | Version(s) |
| ----------- | ----------- | ----------- |
ARAGORN|detects tRNA and tmRNA genes.|1.2.38-foss-2019b
AUGUSTUS|Augustus predicts genes in eukaryotic genomic sequences.|3.3.3-foss-2019b
BamTools|BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files|2.5.1-intel-2019b 2.5.1-GCC-8.3.0
BCFtools|BCFtools are a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart, BCF|1.10.2-intel-2019b 1.10.2-GCC-8.3.0
BEDTools|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.|2.28.0-intel-2019b
BioPerl|Bioperl 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.|1.7.2-GCCcore-8.3.0
BLASR|BLASR (Basic Local Alignment with Successive Refinement) is used for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error.|5.3.3-gompi-2019b
BLAST+|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.|2.10.0-gompi-2019b
BLASTDB|BLAST search pages under the Basic BLAST section of the NCBI BLAST home page (http://blast.ncbi.nlm.nih.gov/) use a standard set of BLAST databases for nucleotide, protein, and translated BLAST searches.|v5
Bowtie|Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.|1.2.3-GCC-8.3.0
Bowtie2|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.|2.3.5.1-GCC-8.3.0
BWA|Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.|0.7.17-intel-2019b
canu|Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).|1.9-GCCcore-8.3.0-Java-11
DIAMOND|Diamond is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity.|0.9.32-GCC-8.3.0
FastQC|FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.|0.11.9-Java-11
GATK|The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV).|4.1.4.1-GCCcore-8.3.0-Java-11 3.8-Java-1.8.0_241
GMAP-GSNAP|GMAP is a tools for rapidly and accurately mapping and aligning cDNA sequences to genomic sequences.|2020-04-08-GCC-8.3.0
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. This is a GPU enabled build, containing both MPI and thread MPI binaries.|2019.5-fosscuda-2019b
HISAT2|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).|2.2.0-foss-2019b
HMMER|HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models|3.2.1-gompi-2019b
HTSlib|A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix|1.10.2-GCC-8.3.0
IQ-TREE|Efficient phylogenomic software by maximum likelihood|1.6.12-intel-2019b
Infernal|Infernal (“INFERence of RNA ALignment”) is for searching DNA sequence databases for RNA structure and sequence similarities.|1.1.3-intel-2019b
LAMMPS|LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It’s an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.|3Mar2020-foss-2019b-Python-3.7.4-kokkos
LASTZ|LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by high-throughput sequencing technologies such as Roche 454|1.04.03-foss-2019b
MAFFT|MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate’ for alignment of < ~200 sequences), FFT-NS-2 (fast; for alignment of < ~30000 sequences), etc|7.453-iccifort-2019.5.281-with-extensions
minimap2|Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the SAM format|2.17-GCC-8.3.0
ncbi-vdb|The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.|2.10.0-foss-2019b
NGS|Here we provide a general workflow for NGS data analysis with RNA-Seq, ChIP-Seq and RRBS-Seq (Reduced Representation of bisulfite sequencing, a cost effecient alternative to whole genome bisulfite sequencing).|2.10.0-GCCcore-8.3.0
PHYLIP|PHYLIP is a package for inferring phylogenies.|3.697-GCC-8.3.0
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. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.|2.21.6-Java-11
Pilon|Pilon is a software tool which can be used to automatically improve draft assemblies find variation among strains, including large event detection.|1.23-Java-11
RAxML|Randomized Axelerated Maximum Likelihood based inference of large phylogenetic trees|8.2.12-intel-2019b-hybrid-avx2
Racon|Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies|1.4.13-GCCcore-8.3.0
R-bundle-Bioconductor|This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects|3.10-fosscuda-2019b-R-3.6.2
 Ray|Ray is a parallel de novo genome assembler that utilises the message-passing interface everywhere and is implemented using peer-to-peer communication. Ray is free software distributed under the terms of the GNU General Public License, version 3 (GPLv3). Ray is implemented using RayPlatform, a message-passing-interface programming framework.|2.3.1-iimpi-2019b
RepeatMasker|RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).|4.0.9-p2-gompi-2019b-HMMER
SAMtools|SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.|1.10-GCC-8.3.0 1.9-intel-2019b
SNAP|snap: Semi-HMM-based Nucleic Acid Pars|4.6.0-foss-2019b-Perl-5.30.0
SPAdes|SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads.|3.14.0-GCC-8.3.0
STAR|Spliced Transcripts Alignment to a Reference|2.7.3a-GCC-8.3.0
TRF|Tandem repeats finder: a program to analyze DNA sequences. Legacy version.|4.09-linux64
Trinity|Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data.|2.8.5-GCC-8.3.0-Java-11
VCFtools|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.|0.1.16-GCC-8.3.0
Unicycler|Unicycler is an assembly pipeline for bacterial genomes.|0.4.8-foss-2019b-Python-3.7.4

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