Biowulf High Performance Computing at the NIH
Application updates in the last 3 months
To see all versions available for any application, use module avail application_name
All centrally-installed applications are listed on the Applications page
Updated Application
18 Oct 2019 Jacquard updated to version 0.4.2
Jacquard makes it easier to analyze multi-patient tumor-normal datasets especially when using multiple vairant callers. It transforms the dialects of different variant callers into a controlled vocabulary of tags with a consistent representation of values. Furthermore, it intelligently merges VCFs from different patients and callers to create a single, unified VCF across your dataset.
18 Oct 2019 spliceai-wrapper updated to version 0.1.0
Spliceai-wrapper is a wrapper for Illumina SpliceAI that caches results
18 Oct 2019 TPMCalculator updated to version 0.0.3
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
17 Oct 2019 Matlab updated to version 2019b
MATLAB is an interactive software package for scientific and engineering numeric computation. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an environment where problems and solutions are expressed just as they are written mathematically.
17 Oct 2019 viennarna updated to version 2.4.14
RNA Secondary Structure Prediction and Comparison
17 Oct 2019 Rstudio updated to version 1.2.5001
RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
16 Oct 2019 cryolo updated to version 1.5.3
Automated particle picker for cryo-EM
16 Oct 2019 BAMSurgeon updated to version 1.2
Tools for adding mutations to existing .bam files; used for testing mutation callers
15 Oct 2019 vg updated to version 1.19.0
Tools for working with genome variation graphs
15 Oct 2019 EMAN2 updated to version 2.31
EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.
11 Oct 2019 snp-sites updated to version 2.4.1
Rapidly extracts SNPs from a multi-FASTA alignment
11 Oct 2019 ariba updated to version 2.14.4
Antimicrobial resistance identification.
10 Oct 2019 dynamo updated to version 1.4.01
Dynamo is a software environment for subtomogram averaging of cryo-EM data.
8 Oct 2019 gubbins updated to version 2.3.4
Gubbins is an algorithm that iteratively identifies loci containing elevated densities of base substitions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
7 Oct 2019 glnexus updated to version 1.1.11
Joint variant calling for large cohort sequencing
7 Oct 2019 crystfel updated to version 0.8.0.71809b358a2
CrystFEL is a suite of programs for processing diffraction data acquired serially in a snapshot manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source.
4 Oct 2019 pilon updated to version 1.23
Pilon is a software tool which can be used to: 1) Automatically improve draft assemblies 2) Find variation among strains, including large event detection
4 Oct 2019 unicycler updated to version 0.4.8
Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline.
3 Oct 2019 chance updated to version 1.0
CHANCE performs CHiP-seq analytics and confidence estimation.
3 Oct 2019 Acemd updated to version 2019-10-02
ACEMD is a high performance molecular dynamics code for biomolecular systems designed specifically for NVIDIA GPUs. Simple and fast, ACEMD uses very similar commands and input files of NAMD and output files as NAMD or Gromacs.
2 Oct 2019 biobambam2 updated to version 2.0.144
Tools for early stage alignment file processing.
2 Oct 2019 VEP updated to version 98
VEP (Variant Effect Predictor) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
2 Oct 2019 smrtanalysis updated to version 8.0.0
SMRT® Analysis is a bioinformatics software suite available for analysis of DNA sequencing data from Pacific Biosciences’ SMRT technology. Users can choose from a variety of analysis protocols that utilize PacBio® and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.
1 Oct 2019 pychopper updated to version 2.0.3
Pychopper v2 is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads.
1 Oct 2019 mdtraj updated to version 1.9.3
MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories and perform a variety of analyses, including fast RMSD, solvent accessible surface area, hydrogen bonding, etc.
27 Sep 2019 visidata updated to version 1.5.2
VisiData is an interactive multitool for tabular data
24 Sep 2019 Chimera updated to version 1.14.0
Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
24 Sep 2019 TVC updated to version 5.10.1
TVC is the standalone Torrent Variant Caller, part of the Ion Torrent Suite.
24 Sep 2019 parallel updated to version 20190922
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
24 Sep 2019 stringtie updated to version 2.0.3
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It is primarily a genome-guided transcriptome assembler, although it can borrow algorithmic techniques from de novo genome assembly to help with transcript assembly.
24 Sep 2019 picard updated to version 2.20.8
Picard comprises 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. Both SAM text format and SAM binary (BAM) format are supported.
23 Sep 2019 snaptools updated to version 1.4.8
A module for working with snap files in Python.
23 Sep 2019 STAR-Fusion updated to version 1.7.0
Transcript fusion detection
23 Sep 2019 cromwell updated to version 46
A Workflow Management System geared towards scientific workflows.
23 Sep 2019 mash updated to version 2.2
mash is a command line tool and library to provide fast genome and metagenome distance estimation using MinHash. Only command line tool is installed
23 Sep 2019 globus-cli updated to version 1.11.0
Globus command line interface
23 Sep 2019 golang updated to version 1.13
The Go programming language
23 Sep 2019 git updated to version 2.23.0
Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
20 Sep 2019 hyphy updated to version 2.5.1
HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning.
17 Sep 2019 BEAST updated to version 1.10.4,2.6.1
BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences.
17 Sep 2019 Genome Browser updated to version 388
The Genome Browser Mirror Fragments is a mirror of the UCSC Genome Browser. The URL is https://hpcnihapps.cit.nih.gov/genome. Users can also access the MySQL databases, supporting files directly, and a huge number of associated executables.
17 Sep 2019 mixcr updated to version 3.0.10
MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data.
17 Sep 2019 flye updated to version 2.5
Fast and accurate de novo assembler for single molecule sequencing reads
17 Sep 2019 cutadapt updated to version 2.5
cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data.
17 Sep 2019 bedtools updated to version 2.29.0
The BEDTools utilities allow one to address common genomics tasks such finding feature overlaps and computing coverage. In addition, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together.
17 Sep 2019 binlorry updated to version 1.1.0
BinLorry is a tool for binning and filtering sequencing reads into distinct files. Reads can be binned and filtered by any attributes encoded in their headers, documented in a CSV file or by length.
16 Sep 2019 medaka updated to version 0.8.1
medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly.
16 Sep 2019 smoldyn updated to version 2.61
Smoldyn is a particle-based spatial stochastic simulator. Molecules are represented by point-like particles in 1-, 2-, or 3-dimensional continuous space. Molecules diffuse by Brownian motion, react when they collide into each other, and interact with surfaces (e.g. membranes) in a variety of realistic ways.
12 Sep 2019 pomoxis updated to version 0.2.3
Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing. Notably tools are included for generating and analysing draft assemblies. Many of these tools are used by the research data analysis group at Oxford Nanopore Technologies.
10 Sep 2019 fmriprep updated to version 1.5.0
A Robust Preprocessing Pipeline for fMRI Data
10 Sep 2019 ctatmutations updated to version 2.0.1
Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
10 Sep 2019 seqkit updated to version 0.10.2
A cross-platform toolkit for FASTA/Q file manipulation
10 Sep 2019 Katuali updated to version 20190821
Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data.
10 Sep 2019 PartekFlow updated to version 8.0.19.0904
Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing.
9 Sep 2019 rfmix updated to version 2.0
Local Ancestry and Admixture Inference
9 Sep 2019 CCP4 updated to version 7.0.076
CCP4 is a suite of programs for protein crystallography and structural biology.
6 Sep 2019 broccoli updated to version 1.0.1
Pipeline for fast analysis of fMRI data
6 Sep 2019 SimNIBS updated to version 3.0.6
SimNIBS is a free software package for the Simulation of Non-invasive Brain Stimulation. It allows for realistic calculations of the electric field induced by transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS).
5 Sep 2019 dcm2niix updated to version 1.0.20190902
DICOM to NIfTI converter
5 Sep 2019 tvb updated to version 1.5.9
The Virtual Brain (TVB) scientific library has the purpose of offering modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains
4 Sep 2019 3DSlicer updated to version 4.10.2
A software platform for the analysis (including registration and interactive segmentation) and visualization (including volume rendering) of medical images and for research in image guided therapy.
4 Sep 2019 GATK updated to version 4.1.3.0
GATK, from the Broad Institute, is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.
4 Sep 2019 mango updated to version 4.1
Mango (Multi-image Analysis GUI) is a viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes.
4 Sep 2019 GAMESS updated to version 30Jun19-R1-sockets
GAMESS is a general ab initio quantum chemistry package.
3 Sep 2019 vartrix updated to version 1.1.4
VarTrix is a software tool for extracting single cell variant information from 10x Genomics single cell data.
3 Sep 2019 hrdetect updated to version 20190829
Hrdetect is a tool for detection and analysis of homologous recombination deficiency signatures. It was developed to accurately detect BRCA1/BRCA2-deficient samples.
29 Aug 2019 guppy updated to version 3.2.2
Local accelerated basecalling for Nanopore data
28 Aug 2019 MVAPICH2 updated to version 2.3.2
MPI implementation for Infiniband
27 Aug 2019 rseqc updated to version 3.0.0
Rseqc comprehensively evaluate RNA-seq datasets generated from clinical tissues or other well annotated organisms such as mouse, fly and yeast.
27 Aug 2019 sortmeRNA updated to version 3.0.3
SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering. The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files specified by the user.
26 Aug 2019 suppa updated to version 2.3
Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
26 Aug 2019 STAR updated to version 2.7.2a
Spliced Transcripts Alignment to a Reference
23 Aug 2019 magicblast updated to version 1.5.0
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.
23 Aug 2019 IGVTools updated to version 2.6.2
IGVTools provides utilities for working with ascii file formats used by the Integrated Genome Viewer. The files can be sorted, tiled, indexed, and counted.
23 Aug 2019 IGV updated to version 2.6.2
The Integrative Genomics Viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
22 Aug 2019 Trinotate updated to version 3.2.0
Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
21 Aug 2019 boost updated to version 1.70
Boost provides free peer-reviewed portable C++ source libraries. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.
21 Aug 2019 Rosetta updated to version 2019.31
The Rosetta++ software suite can perform de novo protein structure predictions, identify low free energy sequences for target protein backbones, predict the structure of a protein-protein complex from the individual structures of the monomer components, incorporate NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction, and more...
20 Aug 2019 snippy updated to version 4.4.1
snippy is a tool for rapid haploid variant calling and core genome alignment
20 Aug 2019 SRST2 updated to version 0.2.0
SRST2 is a a read mapping-based tool for rapid molecular typing of bacterial pathogens. It allows fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment.
13 Aug 2019 king updated to version 2.2.3
Quick Links Documentation Notes Interactive job Batch job Swarm of jobs KING is a toolset to explore genotype data from a genome-wide association study (GWAS) or a sequencing project. KING can be used to check family relationship and flag pedigree errors by estimating kinship coefficients and inferring IBD segments for all pairwise relationships.
13 Aug 2019 scanpy updated to version 1.4.4
Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
8 Aug 2019 nodejs updated to version 10.16.2
Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs
7 Aug 2019 google-cloud-sdk updated to version 257.0.0
Google Cloud SDK is a set of tools that you can use to manage resources and applications hosted on Google Cloud Platform. These include the gcloud, gsutil, and bq command line tools. See docs at https://cloud.google.com/sdk/docs/how-to.
Type 'module load google-cloud-sdk' to use on Biowulf.
6 Aug 2019 CANDLE updated to version main
Open-source software platform providing highly scalable deep learning methodologies, including intelligent hyperparameter optimization.
3 Aug 2019 mriqc updated to version 0.15.1
MRIQC is an MRI quality control tool
2 Aug 2019 READemption updated to version 0.5.0
RNA-Seq pipeline including alignment, coverage tracks, quantitation, and differential expression analysis.
2 Aug 2019 segemehl updated to version 0.3.4
Segemehl is a short read aligner that allows local alignment and can align reads obtained after bisulfite treatment.
31 Jul 2019 fusioncatcher updated to version 1.10
FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq) from diseased samples.
31 Jul 2019 picrust updated to version 2.1.4-b
PICRUSt is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.
30 Jul 2019 cellranger updated to version 3.1.0
Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
30 Jul 2019 Intel Compiler Suite updated to version 2019.4.243
Intel Compiler Suite for Linux. Includes C/C++ and Fortran compilers. Also includes the Math Kernel Library, Integrated Performance Primitives and Thread Building Blocks.
23 Jul 2019 mutsig2cv updated to version 3.11
mutsig2cv analyzes somatic point mutations discovered in DNA sequencing, identifying genes mutated more often than expected by chance.
Scientific Databases updated in last 3 months
For a full list of scientific databases available on the NIH HPC systems, see this page

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