Software Center

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-efficient 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 Portable 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