Pittsburgh Supercomputing Center 

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

PSCBridges

Allocation requests now being accepted.     More information  

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
Abinit Calculates electronic density and derived properties of materials (incl. molecules, surfaces & solids) within DFT using pseudopotentials and a planewave or wavelet basis Chemistry
Computational chemistry
Greenfield
ABySS Parallel assembler for short read sequence data Bioinformatics Greenfield
ANSYS General purpose finite element modeling package Engineering
Multiphysics
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 Greenfield
Bedtools Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format Bioinformatics 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. See related tool Bowtie2. Bioinformatics Greenfield
BioU
Bowtie2 Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie. Bioinformatics Greenfield
BWA Fast light-weight tool that aligns relatively short sequences to a sequence database Bioinformatics Greenfield
BioU
C, C++ Programming languages Programming languages, libraries and tools Greenfield
Celera Assembler De novo WGS DNA sequence assembler Bioinformatics BioU
Cmake Tools to control the compilation process, build, test and package software Programming languages, libraries and tools Greenfield
CUDA Parallel computing platform and API model  Programming languages, libraries and tools Greenfield
Cutadapt Tool to remove adapter sequences from high-throughput sequencing data Bioinformatics Greenfield
Delly Integrated split-read and paired-end structural variant discovery and genotyping method suited for massively parallel sequencing data Bioinformatics Greenfield
Discovar de novo Large (and small) de novo genome assembler Bioinformatics Greenfield
Ea-utils Command-line tools for processing biological sequencing data Bioinformatics Greenfield
Eigen C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms Programming languages, libraries and tools Greenfield
Exonerate Generic tool for sequence comparison Bioinformatics Greenfield
FastQC Quality control tool for high throughput sequence data Bioinformatics Greenfield
FASTX Toolkit Command line tools for Short-Reads FASTA/FASTQ files preprocessing Bioinformatics Greenfield
FFTW3 C subroutine library for computing the DFT in one or more dimensions, of arbitrary input size, of both real and complex data   Greenfield
FLASh Fast and accurate tool to merge paired-end reads from NGS experiments Bioinformatics Greenfield
Flexbar Flexible barcode and adapter removal for sequencing platforms Bioinformatics Greenfield
Fortran Programming language Programming languages, libraries and tools Greenfield
GATK Genome Analysis Toolkit, for high-throughput sequencing data Bioinformatics Greenfield
GlimmerHMM Eukaryotic Gene-Finding System based on a GHMM Bioinformatics BioU
Glimmer3 System for finding genes in microbial DNA, especially the genomes of bacteria, archaea and viruses Bioinformatics BioU
HMMER Biosequence analysis using profile hidden Markov models Bioinformatics Greenfield
HTSeq Analysis of high-throughput sequencing data with Python Bioinformatics Greenfield
Java Programming language Programming languages, libraries and tools Greenfield
LAMMPS Classical molecular dynamics code Molecular dynamics
Chemistry
Greenfield
LS-DYNA General purpose transient dynamic finite element program Finite element solver Greenfield
MACS Model-based Analysis of ChIP-Seq, for identifying transcript factor binding sites Bioinformatics Greenfield
MAFFT Multiple sequence alignment program Bioinformatics Greenfield
MaSuRCA Whole genome assembly, combining the efficiency of the de Bruijn graph and Overlap-Layout-Consensus approaches Bioinformatics Greenfield
MATLAB High-level language and interactive environment, performs computationally intensive tasks faster than traditional 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  
MetaVelvet Extension of Velvet assembler to de novo metagenome assembly from short sequence reads Bioinformatics Greenfield
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
MPI Message Passing Interface. Both Intel MPI and Open MPI are available. Library/MPI Greenfield
MUSCLE MUltiple Sequence Comparison by Log- Expectation Bioinformatics Greenfield
MVAPICH Library exploiting novel features and mechanisms of high-performance networking technologies. 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
PAPI Performance API, specifies a API for accessing hardware performance counters Performance measurement Greenfield
Perl Programming language Programming languages, libraries and tools Greenfield
PETSc Suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations Libraries/math
Mathematics
Greenfield
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 Bioinformatics Greenfield
BioU
Prodigal Open source lightweight microbial genefinding program Bioinformatics Greenfield
BioU
Python (including the matplotlib library) Powerful, object-oriented programming language Programming languages, libraries and tools Greenfield
Quantum Espresso Integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale Computational chemistry
Computational materials science
Greenfield
R (including the ggplot2 package) Language and environment for statistical computing and graphs Programming languages, libraries and tools
Statistics
Greenfield
Ray Parallel de novo genome assembly using MPI Bioinformatics Greenfield
RNA-SeQC Java program, computes a series of quality control metrics for RNA-seq data Bioinformatics Greenfield
RSEM Estimates gene and isoform expression levels from RNA-Seq data Bioinformatics Greenfield
SAMtools Utilities for manipulating alignments in SAM format Bioinformatics 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 Library/math
Mathematics
Greenfield
Scythe Adapter/contaminant removal tool for FASTQ files Bioinformatics Greenfield
SEECER Sequencing error correction algorithm for RNA-seq data sets Bioinformatics Greenfield
Sickle Windowed adaptive trimming tool for FASTQ files Bioinformatics Greenfield
SLEPc Library to solve large scale sparse eigenvalue problems on parallel computers, an extension of PETSc Library/math
Mathematics
Greenfield
SNAP General purpose gene finding program suitable for both eukaryotic and prokaryotic genomes Bioinformatics BioU
SomaticSniper Program to identify single nucleotide positions which differ between tumor and normal cells Bioinformatics BioU
Strelka Somatic variant calling workflow for matched tumor-normal samples Bioinformatics Greenfield
SWIG Tool that connects programs written in C and C++ with a variety of other languages, including Python, Java and R. Programming languages, libraries and tools Greenfield
TopHat Fast splice junction mapper for RNA-Seq reads Bioinformatics 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. Bioinformatics Greenfield
Trinity Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data Bioinformatics Greenfield
BioU
UCSC Utilities Tools and utilities created by the UCSC Genome Bioinformatics Group Bioinformatics Greenfield
Varscan Detects variants in NGS data Bioinformatics Greenfield
VCFtools Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files Bioinformatics Greenfield
Velvet De novo genomic assembler specially designed for short read sequencing technologies Bioinformatics Greenfield
BioU
VTune Performance profiler for OpenMP applications Programming languages, libraries and tools Greenfield
WGS See Celera assembler Bioinformatics Greenfield

 

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