Available software:

Coming soon: software list will be searchable and filtered by category.

Job Scheduling:

  • slurm - Resource manager for sending jobs to the cluster
  • openmpi - Open Source MPI implementation for multicore jobs

Genomics:

  • bbmap - Short read aligner, and other bioinformatic tools
  • bcftools - Utilities for variant calling and manipulating VCFs and BCFs
  • bedtools2 - A powerful toolset for genome arithmetic
  • bioawk - awk for several common biological data formats
  • bowtie - An ultrafast, memory-efficient short read aligner
  • bowtie2 - An ultrafast and memory-effieient tool for aligning sequencing read to long reference sequences
  • bwa - A package for mapping low-divergent sequences against a large reference genome
  • cisa - Contig Integrator for Sequence Assembly of Bacterial Genomes
  • clustal-omega - Multiple Sequence Alignment that uses guide trees and HMM profile
  • cutadapt - Finds and removes adapter sequences, primers, poly-A tails and others from high-throughput sequencing reads
  • ddocent - Interactive bash wrapper to QC, assemble, map, and call SNPs from double digest RAD data
  • diyabc - Comprehensive analysis of population history using approximate Bayesian computation on DNA polymorphism data
  • edena - de novo short reads assembler
  • exabayes - A tool for Bayesian phylogenetic analyses
  • fastqc - A quality control application for high throughput sequence data
  • fasttree - Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
  • fastx_toolkit - A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
  • flash - A very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments
  • gapfiller - Reliably close gaps within scaffolds using paired reads
  • igv - Integrative Genomics Viewer
  • masurca - MaSuRCA Genome assembler
  • megan - MEtaGenome ANalyzer
  • migrate - Estimates effective population sizes and migration rates
  • mira - Sequence assembler and sequence mapping
  • mothur - Software to fill the bioinformatics needs of the microbial ecology community
  • mugsy - Multiple whole genome aligner
  • orthomclsoftware - OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences
  • perl - The PERL program with bio programs
  • phylib - Programs for inferring phylogenies
  • phyml - Phylogeny software based on the maximum-likelihood principle
  • prinseq-lite - filter, reformat, or trim your genomic and metagenomic sequence data
  • prokka - software tool for the rapid annotation of prokaryotic genomes
  • python/2 - python interpreter with bio routines added
  • qiime - bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data
  • R - The R language with bio routines added
  • raxml - standard tool for Maximum-likelihood based phylogenetic inference
  • samtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
  • scythe - uses a Naive Bayesian approach to classify contaminant substrings in sequence reads
  • seastar - package of open-source tools supporting the construction of analysis pipelines for environmental next-generation sequencing data
  • seqtk - fast and lightweight tool for processing sequences in the FASTA or FASTQ format
  • sickle - a windowed adaptive trimming tool for FASTQ files using quality
  • spades - St. Petersburg genome assembler
  • sspace/longread - designed to upgrade incomplete draft genomes using single molecule sequences
  • sspace/standard - program for scaffolding pre-assembled contigs using NGS paired-read data
  • star - Spliced Transcripts Alignment to a Reference
  • structure - package for using multi-locus genotype data to investigate population structure
  • tophat - fast splice junction mapper for RNA-Seq reads
  • trimm_galore - a wrapper script to automate quality and adapter trimming as well as quality control
  • trimmomatic - a flexible trimmer for Illumina sequence data
  • trinityrnaseq - assembles transcript sequences from Illumina RNA-Seq data
  • velvet - algorithms for de novo short read assembly using de Bruijn graphs

Scientific:

  • grads - Grid Analysis and Display System
  • gromacs - A versatile package to perform molecular dynamics
  • idl - A scientific programming language used to extract meaningful visualizations from complex numerical data
  • LAStools - A stand-alone toolset for Airborne Lidar Data
  • matlab - A high-level language and interactive environment
  • ncl - NCAR Command Language
  • nco - standalone command-line programs that take netCDF files as input
  • vsfm - 3D reconstruction using structure from motion

Development:

  • acml - AMD Core Math Library (for legacy apps)
  • ant - Apache Ant is a Java library tool
  • atlas - Automatically Tuned Linear Algebra Software
  • blacs - Basic Linear Algebra Communication Subprograms
  • blas - Basic Library Algebra Software
  • boost - peer-reviewed portable C++ source library
  • cuda65 - Parallel Computing Platform for GPUs
  • eigen - C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms
  • fftw2 & fftw3 - C subroutine library for computing the discrete Fourier transform
  • gcc - C, C++, and FORTRAN gnu compilers
  • gdal - Geospatial Data Abstraction Library
  • globalarrays - A Partitioned Global Address Space (PGAS) programming model
  • hadoop - A software library that allows for the distributed processing of large data sets
  • hdf5/hdf5_18 - A completely new Hierarchical Data Format product
  • htslib - A C library for reading/writing high-throughput sequencing data
  • intel/compiler - The c/c++ and fortran intel compilers
  • intel/mkl - Intel Math Kernel Library
  • lapack - Linear Algebra library package
  • libnabo - A fast K Nearest Neighbour library for low-dimensional spaces
  • mpich - High-Performance Protable MPI
  • mvapich/mvapich2 - Open source implementation of MPI
  • netcdf - Network Common Data Formats for array-oriented scientific data
  • netcdf-fortran - C, Fortran, and parallel versions of NetCDF
  • node - An asynchronous event driven framework
  • opencv - This was designed for computational efficiency and real-time applications
  • oracle/java - The Java interpreter
  • scalapack - Scalable Linear Algebra PACKage
  • viennacl - open-source linear algebra library for computations on many-core architectures (GPUs, MIC) and multi-core CPUs

Developers, get this list as XML: software.xml