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
13 Aug 2019 Rosetta updated to version 2019.22
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...
13 Aug 2019 VEP updated to version 97
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.
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.
6 Aug 2019 picard updated to version 2.20.5
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.
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.
1 Aug 2019 fmriprep updated to version 1.4.1
A Robust Preprocessing Pipeline for fMRI Data
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.
30 Jul 2019 stringtie updated to version 1.3.6
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.
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.
23 Jul 2019 parallel updated to version 20190722
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
19 Jul 2019 bigSCale2 updated to version 20190729
bigSCale is a complete framework for the analysis and visualization of single cell data. It allows to cluster, phenotype, perform pseudotime analysis, infer gene regulatory networks and reduce large datasets in smaller datasets with higher quality.
18 Jul 2019 transabyss updated to version 2.0.1
Trans-ABySS is a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
17 Jul 2019 globus-cli updated to version 1.10.1
Globus command line interface
15 Jul 2019 MEGAHIT updated to version 1.2.6.1
MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG construction.
11 Jul 2019 nvchecker updated to version 1.4.4
nvchecker (short for new version checker) is for checking if a new version of some software has been released.
10 Jul 2019 snakemake updated to version 5.5.2
Snakemake aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style. It is well suited for bioinformatic workflows.
9 Jul 2019 bowtie updated to version 1.2.3
bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.
8 Jul 2019 ChromHMM updated to version 1.19
ChromHMM is software for learning and characterizing chromatin states.
8 Jul 2019 salmon updated to version 0.14.1
a tool for quantifying the expression of transcripts using RNA-seq data.
3 Jul 2019 vcftools updated to version 0.1.16
VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc.
3 Jul 2019 vsearch updated to version 2.13.6
VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
2 Jul 2019 qcat updated to version 1.0.6
qcat is Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
28 Jun 2019 nanopolish updated to version 0.11.1
nanopolish is a software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).
28 Jun 2019 mothur updated to version 1.42.3
mothur is a tool for analyzing 16S rRNA gene sequences generated on multiple platforms as part of microbial ecology projects.
27 Jun 2019 Meryl updated to version 0.0
Meryl: a genomic k-mer counter (and sequence utility) with nice features. It is built into the Celera Assembler and is also available as a stand-alone application. Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order.
26 Jun 2019 xcpengine updated to version 1.0rc1
xpcEngine performs denoising and estimation of Functional Connectivity on fMRI datasets
26 Jun 2019 deeptools updated to version 3.3.0
deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from deep-sequencing DNA sequencing experiments.
21 Jun 2019 metabat updated to version 2.13
MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data
21 Jun 2019 viennarna updated to version 2.4.13
RNA Secondary Structure Prediction and Comparison
19 Jun 2019 homer updated to version 4.10.4
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis.
18 Jun 2019 spades updated to version 3.13.1
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
14 Jun 2019 MotionCor2 updated to version 1.2.6
MotionCor2 is a multi-GPU accelerated program that provides iterative, patch-based motion detection combining spatial and temporal constraints and dose weighting for both single particle and tomographic cryo-electon microscopy images.
13 Jun 2019 smrtanalysis updated to version 7.0.1
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.
13 Jun 2019 Scipion updated to version 2.0.0
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.
12 Jun 2019 singularity updated to version 3.2.1
Singularity is a container platform focused on supporting ``Mobility of Compute``. It allows users to emulate, and share custom Linux environments allowing for the creation of self-contained development stacks.
12 Jun 2019 purge_haplotigs updated to version 1.1.0
purge_haplotigs is a pipeline to help with curating heterozygous diploid genome assemblies.
11 Jun 2019 Comsol updated to version 5.4.0.388
The COMSOL Multiphysics engineering simulation software environment facilitates all steps in the modeling process − defining your geometry, meshing, specifying your physics, solving, and then visualizing your results.
10 Jun 2019 CCP4 updated to version 7.0.074
CCP4 is a suite of programs for protein crystallography and structural biology.
10 Jun 2019 RELION updated to version 3.0.7
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
7 Jun 2019 KrakenUniq updated to version 0.5.8
KrakenUniq is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It combines the fast k-mer-based classification of Kraken (Wood and Salzberg, Genome Biology 2014) with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory.
6 Jun 2019 Schrodinger updated to version 2019.2
A limited number of Schrödinger applications are available on the Biowulf cluster through the Molecular Modeling Interest Group. Most are available through the Maestro GUI.
5 Jun 2019 STAR-Fusion updated to version 1.6.0
Transcript fusion detection
5 Jun 2019 freebayes updated to version 1.3.1
Bayesian haplotype-based polymorphism discovery and genotyping
4 Jun 2019 umitools updated to version 1.0.0
tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
3 Jun 2019 hgvs updated to version 1.3.0
The hgvs package provides a Python library to facilitate the use of genome, transcript, and protein variants that are represented using the Human Genome Variation Society (varnomen) recommendations. To use, type module load hgvs prior to calling python.
3 Jun 2019 vcf2maf updated to version 1.6.17
A smarter, more reproducible, and more configurable tool for converting a VCF to a MAF.
31 May 2019 BETA updated to version 1.0.7
Binding and expression target analysis (BETA) is a software package that integrates ChIP-seq of TFs or chromatin regulators with differential gene expression data to infer direct target genes. The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression.
29 May 2019 PartekFlow updated to version 8.0.19.0508
Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing.
28 May 2019 LDpred updated to version 1.0.6
LDpred is a Python based software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium (LD).
24 May 2019 guppy updated to version 3.1.5
Local accelerated basecalling for Nanopore data
23 May 2019 turbovnc updated to version 2.2.2
TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads.
22 May 2019 GCC updated to version 9.1.0
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, and Go, as well as libraries for these languages (libstdc++, libgfortran,...)
21 May 2019 QIIME updated to version 2-2019.4
QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data).
20 May 2019 circtools updated to version 1.1.0.8
Circtools is a modular, Python3-based framework for circRNA-related tools that unifies several functionalities in single command line driven software. The command line follows the circtools subcommand standard that is employed in samtools or bedtools. Currently, circtools includes modules for detecting and reconstructing circRNAs, a quick check of circRNA mapping results, RBP enrichment screenings, circRNA primer design, statistical testing, and an exon usage module.
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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