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Software available on PSC systems

 

The Module package

The environment management package Module is essential for running software on PSC systems.  Be sure to check if there is a module for the software you want to use by typing module avail software-name

The module help command lists any additional modules that must also be loaded.  Note that in some cases the order in which these additional modules are loaded matters. 

Documentation on the module command.

You may request that additional software be installed by sending mail to This email address is being protected from spambots. You need JavaScript enabled to view it.

 

 
Software Description Computing Resource
Abinit Calculates electronic density and derived properties of materials (incl. molecules, surfaces & solids) within DFT using pseudopotentials and a planewave or wavelet basis Bridges
Greenfield
ABySS Parallel assembler for short read sequence data Greenfield
AIPS Astronomical Image Processing System Bridges
Anaconda Open data science platform, includes popular Python, R and SCALA packages Bridges
Annovar Functionally annotates genetic variants detected from diverse genomes Bridges
ANSYS General purpose finite element modeling package Bridges
Greenfield
Ant JAVA build tool Greenfield
ATLAS ANSI C and Fortran77 interfaces for the entire BLAS API, and a some of the LAPACK AP Bridges
BAMTools C++ API and toolkit for analyzing and managing BAM files Bridges
Greenfield
BCFTools Utilities for variant calling and manipulating VCFs and BCFs Greenfield
Bedops Tools to address common questions raised in genomics studies Bridges
Greenfield
Bedtools Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format Greenfield
BioU
BLASR Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement Bridges
BLAST Search tool that finds regions of local similarity between nucleotide or protein sequences Bridges
Greenfield
BioU
BLAT Alignment tool like BLAST, but structured differently Bridges
Boost Peer reviewed C++ source libraries Bridges
Greenfield
Bowtie Ultrafast, memory-efficient short read aligner. See related tool Bowtie2. Bridges
Greenfield
BioU
Bowtie2 Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie. Bridges
Greenfield
BWA Fast light-weight tool that aligns relatively short sequences to a sequence database Bridges
Greenfield
BioU
C, C++ Programming languages Bridges
Greenfield
Caffe Deep learning framework Bridges
Canu Fork of the Celera Assembler designed for high-noise single-molecule sequencing Bridges
CDBFASTA FASTA file indexing and retrieval tool Bridges
CD-HIT Tool to cluster and compare protein or nucleotide sequences Bridges
Celera Assembler De novo WGS DNA sequence assembler Bridges
Greenfield
BioU
CFITISO Library of C and Fortran routines for reading and writing data in FITS format. Bridges
Cmake Tools to control the compilation process, build, test and package software Bridges
Greenfield
CUDA Parallel computing platform and API model  Bridges
Greenfield
Cutadapt Tool to remove adapter sequences from high-throughput sequencing data Greenfield
DDT Debugger for C, C++ and Fortran 90 threaded and parallel codes Bridges
Delly Integrated split-read and paired-end structural variant discovery and genotyping method suited for massively parallel sequencing data Greenfield
Desmond High-speed molecular dynamics simulations of biological systems with novel parallel algorithms and numerical techniques for high performance and accuracy Bridges
Detonate DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation Bridges
Greenfield
DIAMOND Alignment tool for aligning short DNA sequencing reads to a protein reference database Bridges
Discovar de novo Large (and small) de novo genome assembler Bridges
Greenfield
DReAMM Designs, renders and animates the output from a MCell simulation  
Ea-utils Command-line tools for processing biological sequencing data Greenfield
Eigen C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms Greenfield
EricScript Computational framework for the discovery of gene fusions in paired end RNA-seq data. Bridges
Exonerate Generic tool for sequence comparison Greenfield
Falcon Collection of genome assembly tools Bridges
FASTA-Splitter Divides a single FASTA file into multiple files Bridges
FASTQ-Splitter Divides a single FASTQ file into multiple files Bridges
FastQC Quality control tool for high throughput sequence data Bridges
Greenfield
FASTX Toolkit Command line tools for Short-Reads FASTA/FASTQ files preprocessing Bridges
Greenfield
FFTW3 C subroutine library for computing the DFT in one or more dimensions, of arbitrary input size, of both real and complex data Bridges
Greenfield
FLASh Fast and accurate tool to merge paired-end reads from NGS experiments Bridges
Greenfield
Flexbar Flexible barcode and adapter removal for sequencing platforms Greenfield
FragGeneScan Finds fragmented genes in short reads and predicts prokaryotic genes in incomplete assemblies or complete genomes Bridges
Fortran Programming language Bridges
Greenfield
FTools Utility programs to create, examine and modify FITS files Bridges
GAMESS Ab initio molecular quantum chemistry Bridges
GATK Genome Analysis Toolkit, for high-throughput sequencing data Greenfield
Gaussian Electronic structure program Bridges
GlimmerHMM Eukaryotic Gene-Finding System based on a GHMM BioU
Glimmer3 System for finding genes in microbial DNA, especially the genomes of bacteria, archaea and viruses BioU
GROMACS Molecular dynamics software primarily designed for biomolecular systems Bridges
HDF5 Data model, library, and file format for storing and managing data Bridges
HISAT2 Fast, sensitive alignment, mapping NGS reads (DNA & RNA) to a population of human genomes or against a single reference genome Bridges
HMMER Biosequence analysis using profile hidden Markov models Bridges
Greenfield
IDBA-TRAN Iterative De Bruijn Graph De Novo Assembler short read assembler for transcriptomes Bridges
IDBA-UD Iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth Bridges
Java Programming language Bridges
Greenfield
khmer Tools to work with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells Bridges
LAMMPS Classical molecular dynamics code Bridges
Greenfield
LevelDB Fast key-value storage library that provides an ordered mapping from string keys to string values. Bridges
LS-DYNA General purpose transient dynamic finite element program Bridges
Greenfield
LSMS Locally Self-consistent Multiple Scattering method, an order-N approach to the calculating the electronic structure of large systems within the local density approximation  
MACS Model-based Analysis of ChIP-Seq, for identifying transcript factor binding sites Greenfield
MAFFT Multiple sequence alignment program Greenfield
MALLET NLP, document classification and other machine learning applications for text Bridges
MaSuRCA Whole genome assembly, combining the efficiency of the de Bruijn graph and Overlap-Layout-Consensus approaches Bridges
Greenfield
MATLAB High-level language and interactive environment, performs computationally intensive tasks faster than traditional languages Bridges
Greenfield
Maven Apache build manager for Java projects Bridges
Greenfield
MAXBIN Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm Bridges
MCell Monte Carlo Cell, simulates the movements and reactions of molecules within and between cells  
MEGAN MEta Genome ANalyzer Bridges
MetaVelvet Extension of Velvet assembler to de novo metagenome assembly from short sequence reads Greenfield
MKL Math Kernel Library, highly optimized and threaded routines for linear algebra, FFTs, vector math and random number generators Bridges
Greenfield
MPI Message Passing Interface. Both Intel MPI and Open MPI are available. Bridges
Greenfield
MUSCLE MUltiple Sequence Comparison by Log- Expectation Greenfield
MVAPICH Library exploiting novel features and mechanisms of high-performance networking technologies. Delivers improved performance and scalability to MPI applications. Greenfield
NAMD Parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems Bridges
NetCDF Software libraries and self-describing, machine-independent data formats supporting the creation, access, and sharing of array-oriented scientific data Bridges
NWCHEM Computes the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density Bridges
OpenFOAM Finite volume CFD package Bridges
OpenMPI High performance message passing library Bridges
Greenfield
PAPI Performance API, specifies a API for accessing hardware performance counters Bridges
Greenfield
Parseltongue Python interface to classic AIPS, Obit, and other task-based data reduction packages Bridges
PBJELLY Highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles Bridges
Perl Programming language Bridges
Greenfield
PETSc Suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations Bridges
Greenfield
Phylosift Tool suite to conduct phylogenetic analysis of genomes and metagenomes Bridges
Picard Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files Bridges
Greenfield
BioU
Pilon Automatically improves draft assemblies and finds variation among strains, including large event detection Bridges
Prodigal Open source lightweight microbial genefinding program Greenfield
BioU
Python (including  matplotlib, numpy, scipy) Powerful, object-oriented programming language Bridges
Greenfield
Quantum Espresso Integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale Bridges
Greenfield
R (including the ggplot2 package) Language and environment for statistical computing and graphs Bridges
Greenfield
Ray Parallel de novo genome assembly using MPI Bridges
Greenfield
RNAmmer Predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences Bridges
RNA-SeQC Java program, computes a series of quality control metrics for RNA-seq data Greenfield
RSEM Estimates gene and isoform expression levels from RNA-Seq data Bridges
Greenfield
Sailfish Alignment-free isoform quantification from RNA-seq reads using lightweight algorithms Bridges
Salmon Tool for fast transcript quantification from RNA-seq data Bridges
SAMtools Utilities for manipulating alignments in SAM format Bridges
Greenfield
BioU
SCOTCH Package and libraries for sequential and parallel graph partitioning, static mapping and clustering, sequential mesh and hypergraph partitioning, and sequential and parallel sparse matrix block ordering Bridges
Greenfield
Scythe Adapter/contaminant removal tool for FASTQ files Bridges
Greenfield
SEECER Sequencing error correction algorithm for RNA-seq data sets Greenfield
Seqtk Toolkit for processing sequences in FASTA/Q formats Bridges
Sickle Windowed adaptive trimming tool for FASTQ files Bridges
Greenfield
SIESTA Performs efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids Bridges
SignalP Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes and eukaryotes Bridges
SLEPc Library to solve large scale sparse eigenvalue problems on parallel computers, an extension of PETSc Greenfield
SNAP General purpose gene finding program suitable for both eukaryotic and prokaryotic genomes BioU
SNVMIX Detects single nucleotide variants from next generation sequencing data Bridges
SomaticSniper Program to identify single nucleotide positions which differ between tumor and normal cells Bridges
BioU
SPAdes St. Petersburg genome assembler, for both standard isolates and single-cell MDA bacteria assemblies Bridges
SRA toolkit Collection of tools and libraries for using data in the INSDC Sequence Read Archives Bridges
Strelka Somatic variant calling workflow for matched tumor-normal samples Bridges
Greenfield
SWIG Tool that connects programs written in C and C++ with a variety of other languages, including Python, Java and R. Greenfield
Tensorflow Machine learning library for numerical computation using data flow graphs Bridges
Theano Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently Bridges
TMHMM Predicts transmembrane helices in proteins Bridges
TopHat Fast splice junction mapper for RNA-Seq reads Bridges
Greenfield
Trim Galore Wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. Extra functionality for MspI-digested RRBS-type libraries. Greenfield
Trimmomatic Fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. Bridges
Trinity Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data Bridges
Greenfield
BioU
Trinotate Annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms Bridges
UCSC Utilities Tools and utilities created by the UCSC Genome Bioinformatics Group Greenfield
UFRaw Utility to read and manipulate raw images from digital cameras Bridges
UNCeqR Method and associated software for discovering somatic mutations using the integration of DNA and RNA sequencing Bridges
Varscan Detects variants in NGS data Bridges
Greenfield
VASP Atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. You must have your own license. PSC can help with installation.
VCFtools Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files Greenfield
Velvet De novo genomic assembler specially designed for short read sequencing technologies Bridges
Greenfield
BioU
VTune Performance analysis tool for serial, multithreaded or MPI applications Bridges
Greenfield
WESTPA Constructs and runs stochastic simulations using the “weighted ensemble” approach of Huber and Kim Bridges
WGS See Celera assembler Bridges
Greenfield
Zlib Data compression library Bridges