Software on Bridges-2

This is an initial list of software to be installed on Bridges-2 for the Early User Program.  Additional applications may be installed as requested. You can request software by using this form:

The Module package

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

module avail software-name

More infomation about the software and their modules is available by typing

module spider software-name

To load the environment for a software package, which defines paths and variables needed to use the software, type

module load software-name

The module help software-name 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
ABySS Parallel assembler for short read sequence data
Anaconda Open data science platform, includes popular Python, R and SCALA packages
ANSYS General purpose finite element modeling package
AOCC AMD compilers for use on the RM nodes
Aspera Allows for rapid transfer of large files and data sets
ATLAS ANSI C and Fortran77 interfaces for the entire BLAS API, and a some of the LAPACK AP
BAMTools C++ API and toolkit for analyzing and managing BAM files
BCFTools Utilities for variant calling and manipulating VCFs and BCFs
BEDOPS Tools to address common questions raised in genomics studies
Bedtools Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format
Bismark Bisulfite read mapper and methylation caller
BLAST Search tool that finds regions of local similarity between nucleotide or protein sequences
BLAT Alignment tool like BLAST, but structured differently
Boost Peer reviewed C++ source libraries
Bowtie Ultrafast, memory-efficient short read aligner. See related tool Bowtie2.
Bowtie2 Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie.
BWA Fast light-weight tool that aligns relatively short sequences to a sequence database
C, C++ Programming languages
Caffe Deep learning framework
CMake Tools to control the compilation process, build, test and package software
CP2K Atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems
CUDA Parallel computing platform and API model
Cutadapt Reads a FASTA or FASTQ file, finds and removes adapters, writes the changed sequence to standard output
DDT Debugger for C, C++ and Fortran 90 threaded and parallel codes
Eigen C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms
FastQC Quality control tool for high throughput sequence data
FASTX Toolkit Tools for preprocessing data from FASTA and FASTQ files
FFTW3 C subroutine library for computing the DFT in one or more dimensions, of arbitrary input size, of both real and complex data
FLASh Fast and accurate tool to merge paired-end reads from NGS experiments
Fortran Programming language
Galaxy Open, web-based platform for data intensive biomedical research.
GATK Genome Analysis Toolkit, for high-throughput sequencing data
Gaussian Electronic structure program
GCC (GNU Compiler Collection) Compiler system supporting various programming languages
GDAL Geospatial Data Abstraction Library
GNU Parallel Shell tool for executing jobs in parallel using one or more computers
GROMACS Molecular dynamics software primarily designed for biomolecular systems
Gurobi Mathematical programming solver
Hadoop Big Data processing framework
HDF5/PHDF5 Data model, library, and file format for storing and managing data and its parallel version
HISAT2 Fast, sensitive alignment, mapping NGS reads (DNA & RNA) to a population of human genomes or against a single reference genome
HMMER Biosequence analysis using profile hidden Markov models
Homer Suite of tools for motif discovery and next-gen sequence analysis
Intel Intel compilers, libraries and MPI implementation
Java Programming language
JPEG Method of lossy compression for digital images
Julia High-level, high-performance dynamic programming language for numerical computing Bridges
Keras Minimalist, highly modular neural networks library written in Python and capable of running on top of either TensorFlow or Theano
LAMMPS Classical molecular dynamics code
LevelDB Fast key-value storage library that provides an ordered mapping from string keys to string values.
MATLAB High-level language and interactive environment, performs computationally intensive tasks faster than traditional languages
Maven Apache build manager for Java projects
MetaPhlAn/ MetaPhlAn 2 Computational tools for profiling the composition of microbial communities from metagenomic shotgun sequencing data
MKL Math Kernel Library, highly optimized and threaded routines for linear algebra, FFTs, vector math and random number generators
MPI Message Passing Interface. Both Intel MPI and Open MPI are available.
MuST ab initio electronic structure calculation
NAMD Parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems
NWCHEM Computes the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density
OnDemand Web browser interface to manage files, submit and track jobs on Briges
OpenBLAS Optimized BLAS library
OpenCV Open source library of several hundred computer vision algorithms
OpenMPI High performance message passing library
Perl Programming language
PGI PGI compilers and Tools
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
pnetCDF High-performance, parallel library for files compatible with netCDF
Prodigal Open source lightweight microbial genefinding program
Protocol buffer Protocol Buffers, method of serializing structured data
Python (including  matplotlib, numpy, scipy) Powerful, object-oriented programming language
Quantum Espresso Integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale
R, RStudio (including the ggplot2 package) Language and environment and an IDE for statistical computing and graphs
RAxML Maximum likelihood phylogeny estimation for interpreting relationships between sets of data
SAMtools Utilities for manipulating alignments in SAM format
Singularity Open-source software container platform
SPAdes St. Petersburg genome assembler – an assembly toolkit with various assembly pipelines
Spark Open source software web application framework and domain-specific language written in Java
SRA toolkit Collection of tools and libraries for using data in the INSDC Sequence Read Archives
STAR-Fusion Uses the STAR aligner to dentify candidate fusion transcripts supported by Illumina reads, maps junction and spanning reads to a reference annotation set
STAR Aligner Spliced Transcripts Alignment to Reference, an alignment tool for RNA sequences
TAU Tuning and Analysis Utilities
TensorFlow Machine learning library for numerical computation using data flow graphs
tmux Terminal multiplexer; create and control multiple terminals
Trinity Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data

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

Electronic structure calculations of solids using DFT

You must have your own license. PSC can help with installation.

Zlib Data compression library
Zoltan Data management services for unstructured, adaptive and dynamic applications