Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing,
communications and data analytics.

Alphabetical list of 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. 

See documentation on the module command for more information.

 

Software Description Category Computing Resource
Annovar Tool  utilizing up-to-date information to functionally annotate genetic variants detected from diverse genomes Bioinformatics Greenfield
Ant JAVA build tool Programming languages, libraries and tools Greenfield
BAMTools C++ API and toolkit for analyzing and managing BAM files Bioinformatics Greenfield
BCFTools Utilities for variant calling and manipulating VCFs and BCFs Bioinformatics Greenfield
Bedops Tools to address common questions raised in genomics studies Bioinformatics
Genomics
Transcriptonomics
Next-generation sequencing
Greenfield
Bedtools Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format Bioinformatics
Genomics
Transcriptonomics
Next-generation sequencing
Greenfield
BioU
Blast Search tool that finds regions of local similarity between nucleotide or protein sequences Bioinformatics BioU
Boost Peer reviewed C++ source libraries Programming languages,libraries and tools Greenfield
Bowtie Ultrafast, memory-efficient short read aligner Bioinformatics
Genomics
Transcriptonomics
Next-generation sequencing
Greenfield
BioU
BWA Fast light-weight tool that aligns relatively short sequences to a sequence database Bioinformatics
Genomics
Next-generation sequencing
Greenfield
BioU
C, C++ Programming languages Programming languages, libraries and tools Greenfield
Celera Assembler De novo whole-genome shotgun (WGS) DNA sequence assembler Genomics
Next-generation sequencing
BioU
Cmake Tools to control the compilation process, build, test and package software Programming languages, libraries and tools Greenfield
CUDA Parallel computing platform and application programming interface (API) model  Programming languages, libraries and tools Greenfield
Cufflinks Assembles transcripts, estimates their abundances and tests for differential expression and regulation in RNA-Seq samples Bioinformatics Greenfield
Cutadapt Tool to remove adapter sequences from high-throughput sequencing data Bioinformatics Greenfield
Eigen C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms Programming languages, libraries and tools Greenfield
FastQC Quality control tool for high throughput sequence data Bioinformatics Greenfield
Fortran Programming language Programming languages, libraries and tools Greenfield
GlimmerHMM Eukaryotic Gene-Finding System based on a Generalized Hidden Markov Model (GHMM) Bioinformatics BioU
Glimmer3 System for finding genes in microbial DNA, especially the genomes of bacteria, archaea and viruses Bioinformatics BioU
Java Programming language Programming languages, libraries and tools Greenfield
Matlab High-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages Programming languages, libraries and tools Greenfield
Maven Apache build manager for Java projects Programming languages, libraries and tools Greenfield
MCell (Monte Carlo Cell), simulates the movements and reactions of molecules within and between cells Computational biology  
MKL Math Kernel Library, highly optimized and threaded routines for linear algebra, FFTs, vector math and random number generators Programming languages, libraries and tools Greenfield
MUSCLE MUltiple Sequence Comparison by Log- Expectation Bioinformatics Greenfield
MVAPICH Library which exploits the novel features and mechanisms of high-performance networking technologies and delivers improved performance and scalability to MPI applications. Programming languages, libraries and tools Greenfield
OpenMPI High performance message passing library Programming languages, libraries and tools Greenfield
Perl Programming language Programming languages, libraries and tools Greenfield
Picard Java-based command-line utilities that manipulate SAM (Sequence Alignment/Map)files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files Bioinformatics
Next-generation sequencing
Greenfield
BioU
Prodigal open source lightweight microbial genefinding program Bioinformatics BioU
Python (including the matplotlib library) Powerful, object-oriented programming language Programming languages, libraries and tools Greenfield
R (including the ggplot2 package) Language and environment for statistical computing and graphs Programming languages, libraries and tools
Statistics
Greenfield
SAMtools Utilities for manipulating alignments in the SAM (Sequence Alignment/Map) format Bioinformatics
Next-generation sequencing
Greenfield
BioU
SNAP General purpose gene finding program suitable for both eukaryotic and prokaryotic genomes Bioinformatics BioU
SomaticSniper Program to identify single nucleotide positions that are different between tumor and normal cells Bioinformatics
Genomics
Transriptonomics
Next-generation sequencing
BioU
TopHat Fast splice junction mapper for RNA-Seq reads Bioinformatics Greenfield
Trinity Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data Bioinformatics
Transcriptonomics
Next-generation sequencing
Greenfield
BioU
Varscan Detects variants in NGS data Bioinformatics
Genomics
Next-generation sequencing
Greenfield
VCFtools Tool which provides easily accessible methods for working with complex genetic variation data in the form of VCF files Bioinformatics
Next-generation sequencing
Greenfield
Velvet De novo genomic assembler specially designed for short read sequencing technologies Bioinformatics
Genomics
Next-generation sequencing
Greenfield
BioU
VTune Performance profiler for OpenMP applications Programming languages, libraries and tools Greenfield

 

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.