High-Performance Computing at the NIH
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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
23 Mar 2018 pvactools updated to version 1.0.2
pVACtools is a cancer immunotherapy suite consisting of pVACseq, pVACfuse, pVACvector
23 Mar 2018 cnvnator updated to version 0.3.3
CNVnator is a tool for CNV discovery and genotyping from depth of read mapping.
23 Mar 2018 ROOT updated to version 6.13.02
The ROOT system provides a set of Object-Oriented frameworks with all the functionality needed to handle and analyse large amounts of data in a very efficient way.
23 Mar 2018 nirvana updated to version 2.0.4
Nirvana provides clinical-grade annotation of genomic variants (SNVs, MNVs, insertions, deletions, indels, and SVs (including CNVs). It can be run as a stand-alone package or integrated into larger software tools that require variant annotation.
23 Mar 2018 Ruby updated to version 2.5.0
A dynamic, open source programming language with a focus on simplicity and productivity
22 Mar 2018 conpair updated to version 10102016
Concordance and contamination estimator for tumor–normal pairs
22 Mar 2018 PePr updated to version 1.1.21
PePr is a ChIP-Seq Peak-calling and Prioritization pipeline that uses a sliding window approach and models read counts across replicates and between groups with a negative binomial distribution.
21 Mar 2018 AdmixTools updated to version 4.1
ADMIXTOOLS is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
21 Mar 2018 bamreadcount updated to version 0.8.0
Bam-readcount generates metrics at single nucleotide positions. There are number of metrics generated which can be useful for filtering out false positive calls.
21 Mar 2018 Julia updated to version 0.6.2
high level, dynamic language for technical computing
20 Mar 2018 rdfind updated to version 1.3.5
rdfind is a program that finds duplicate files. It is useful for compressing backup directories or just finding duplicate files. It compares files based on their content, NOT on their file names. After typing module load rdfind, type man rdfind for more information.
20 Mar 2018 squashfs-tools updated to version 4.3
Squashfs is a highly compressed read-only filesystem for Linux. Squashfs compresses both files, inodes and directories, and supports block sizes up to 1Mbytes for greater compression.
20 Mar 2018 ngsqctoolkit updated to version 2.3.3
A toolkit for the quality control (QC) of next generation sequencing (NGS) data.
20 Mar 2018 singularity updated to version 2.4.5
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.
20 Mar 2018 breakdancer updated to version 1.4.5
provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
19 Mar 2018 viennarna updated to version 2.4.4
RNA Secondary Structure Prediction and Comparison
19 Mar 2018 Ghostscript updated to version 9.22
Ghostscript is an interpreter for the PostScript language and for PDF.
19 Mar 2018 IDBA updated to version 1.1.3
IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics. Most assemblers based on de Bruijn graph build a de Bruijn graph with a specific k to perform the assembling task. For all of them, it is very crucial to find a specific value of k. If k is too large, there will be a lot of gap problems in the graph. If k is too small, there will a lot of branch problems. IDBA uses not only one specific k but a range of k values to build the iterative de Bruijn graph. It can keep all the information in graphs with different k values.
19 Mar 2018 vt updated to version 0.577
vt is a variant tool set that discovers short variants from Next Generation Sequencing data.
19 Mar 2018 PyMOL updated to version 2.1.0
A comprehensive molecular visualization product for rendering and animating 3D molecular structures.
19 Mar 2018 miso updated to version 0.5.4
MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data
15 Mar 2018 homer updated to version 4.9.1
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis.
15 Mar 2018 shapeit updated to version 2.r904
SHAPEIT is a fast and accurate haplotype inference software
15 Mar 2018 minc-toolkit updated to version 1.9.16
This metaproject bundles multiple MINC-based packages that historically have been developed somewhat independently
15 Mar 2018 mafft updated to version 7.394
Multiple alignment program for amino acid or nucleotide sequences
14 Mar 2018 plinkseq updated to version 0.10
library for the analysis of genetic variation data
14 Mar 2018 spades updated to version 3.11.0
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
14 Mar 2018 bam2fastq updated to version 1.1.0
This tool is used to extract raw sequences (with qualities) from bam files.
13 Mar 2018 KAT updated to version 2.4.0-h2
KAT (K-mer Analysis Toolkit) is a suite of tools that analyse Jellyfish hashes or sequence files (fasta or fastq) using kmer counts.
13 Mar 2018 ORFfinder updated to version 0.4.0
ORF finder searches for open reading frames (ORFs) in the DNA sequence you enter. The program returns the range of each ORF, along with its protein translation. Use ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP.
13 Mar 2018 KmerGenie updated to version 1.7044
KmerGenie estimates the best k-mer length for genome de novo assembly.
13 Mar 2018 cnvkit updated to version 0.9.3
Copy number variant detection from targeted DNA sequencing
13 Mar 2018 Maven updated to version 3.5.3
Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.
12 Mar 2018 stringtie updated to version 1.3.4
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.
12 Mar 2018 trimgalore updated to version 0.4.5
Consistent quality and adapter trimming for RRBS or standard FastQ files.
12 Mar 2018 OpenBabel updated to version 2.4.1
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
12 Mar 2018 oases updated to version 0.2.09
oases is a de novo transcriptome assembler based on the Velvet genome assembler core.
12 Mar 2018 PyPy updated to version 5.10.0
PyPy is a fast, compliant alternative implementation of the Python language.
12 Mar 2018 EukRep updated to version 20180308
Microbial eukaryotes are integral components of natural microbial communities and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, eukaryotic genomes shoould be recovered from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. EukRep is a kmer- and SVM-based strategy for eukaryotic sequence identification from environmental samples.
9 Mar 2018 matio updated to version 1.5.12
Matio is an open-source C library for reading and writing binary MATLAB MAT files. This library is designed for use by programs/libraries that do not have access or do not want to rely on MATLAB's shared libraries.
9 Mar 2018 summovie updated to version 1.0.2
Summovie calculates movie frame sums, using the alignment results from a prior run of Unblur.
9 Mar 2018 unblur updated to version 1.0.2
Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion.
9 Mar 2018 Gromacs updated to version 2018
Gromacs is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
8 Mar 2018 deeptools updated to version 3.0.1
deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from deep-sequencing DNA sequencing experiments.
8 Mar 2018 delly updated to version 0.7.8
DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.
8 Mar 2018 Gctf updated to version 1.06
Gctf provides accurate estimation of the contrast transfer function (CTF) for near-atomic resolution cryo electron microscopy (cryoEM) reconstruction using GPUs.
8 Mar 2018 velvet updated to version 1.2.10
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454
8 Mar 2018 GAMESS updated to version 14Feb18-R1-sockets
GAMESS is a general ab initio quantum chemistry package.
8 Mar 2018 peakranger updated to version 1.18
A ChIP-Seq peak caller for narrow and broad peaks
7 Mar 2018 CSD updated to version 5.39
The Cambridge Structural Database is the world repository of small molecule crystal structures.
7 Mar 2018 cellranger updated to version 2.1.1
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.
7 Mar 2018 vcf2maf updated to version 1.6.16
A smarter, more reproducible, and more configurable tool for converting a VCF to a MAF.
7 Mar 2018 BFC updated to version 1.0-7-g69ab176
BFC is a standalone tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.
7 Mar 2018 sratoolkit updated to version 2.9.0
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
7 Mar 2018 picard updated to version 2.17.11
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.
6 Mar 2018 RAxML updated to version 8.2.11
RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML).
6 Mar 2018 snptest updated to version 2.5.4beta3
SNPTEST is a program for the analysis of single SNP association in genome-wide studies. The tests implemented include * Binary (case-control) phenotypes, single and multiple quantitative phenotypes * Bayesian and Frequentist tests * Ability to condition upon an arbitrary set of covariates * Various different methods for the dealing with imputed SNPs. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL.
6 Mar 2018 hgvs updated to version 1.1.1
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.
6 Mar 2018 sambamba updated to version 0.6.7
Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.
6 Mar 2018 NGSutils updated to version 0.5.9
NGSUtils is a suite of software tools for working with next-generation sequencing datasets.
4 Mar 2018 Fiji updated to version 1.51s
Fiji Is Just ImageJ. It is a distribution of ImageJ (and ImageJ2) together with Java, Java3D and a lot of plugins.
2 Mar 2018 EMAN2 updated to version 2.21a
EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.
2 Mar 2018 PyTorch updated to version 0.2.0
PyTotch implements Tensors, which are conceptually identical to the Numpy multidimensional arrays, but, unlike the Numpy arrays, can be used on GPU nodes to accelerate numerical computations. It also implements automatic differentiation to automate the computation of backward passes in neural networks.
1 Mar 2018 GATK updated to version
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.
28 Feb 2018 minimap2 updated to version 2.9
Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR).
28 Feb 2018 Eigen updated to version 3.3.4
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
28 Feb 2018 MUSCLE updated to version 3.8.31
Fast Multiple Sequence Alignment program.
27 Feb 2018 PartekFlow updated to version
Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing.
27 Feb 2018 interproscan updated to version 5.27-66.0
InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.
27 Feb 2018 libarchive updated to version 3.3.2
Multi-format archive and compression library
26 Feb 2018 Acemd updated to version 3212u1
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.
26 Feb 2018 trinity updated to version 2.6.5
Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
26 Feb 2018 htseq updated to version 0.9.1
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
26 Feb 2018 jellyfish updated to version 2.2.7
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
23 Feb 2018 LEMON updated to version 1.3.1
LEMON stands for Library for Efficient Modeling and Optimization in Networks. It is a C++ template library providing efficient implementations of common data structures and algorithms with focus on combinatorial optimization tasks connected mainly with graphs and networks.
23 Feb 2018 glpk updated to version 4.65
The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
23 Feb 2018 salmon updated to version 0.9.1
a tool for quantifying the expression of transcripts using RNA-seq data.
22 Feb 2018 gautomatch updated to version 0.56
Fully automatic acccurate, convenient and extremely fast particle picking for EM
21 Feb 2018 bamliquidator updated to version 1.3
bamliquidator is a set of tools for analyzing the density of short DNA sequence read alignments in the BAM file format.
21 Feb 2018 hap.py updated to version 0.3.7
A set of programs based on htslib to benchmark variant calls against gold standard truth datasets.
20 Feb 2018 Aspera updated to version 3.7..4
High-speed fasp-powered file transfers. Mostly used to download data from NCBI, which has an Aspera server. See the data transfer page for details.
20 Feb 2018 Tcl/Tk updated to version 8.6.3
Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language. Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches.
20 Feb 2018 bedops updated to version 2.4.26
Bedops is a suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets - BEDOPS aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.
20 Feb 2018 digits updated to version 5.0
DIGITS simplifies common deep learning tasks such as managing data, designing and training neural networks on multi-GPU systems, monitoring performance in real time with advanced visualizations, and selecting the best performing model from the results browser for deployment. DIGITS is completely interactive so that data scientists can focus on designing and training networks rather than programming and debugging.
20 Feb 2018 kraken updated to version 1.1
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies
15 Feb 2018 deepvariant updated to version 0.5.1
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
15 Feb 2018 minialign updated to version 0.5.3
fast and accurate alignment tool for PacBio and Nanopore long reads
15 Feb 2018 graphmap updated to version 0.5.2
A highly sensitive and accurate mapper for long, error-prone reads
15 Feb 2018 multiqc updated to version 1.4
aggregates results for various frequently used bioinformatics tools across multiple samples into a nice visual report
15 Feb 2018 SQLite updated to version 3.22.0
SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine.
14 Feb 2018 schism updated to version 1.1.3
Subclonal Hierarchy Inference from Somatic Mutations
14 Feb 2018 Caret updated to version 5.65
Caret is a free, open-source, software package for structural and functional analyses of the cerebral and cerebellar cortex. It is largely deprecated by the Connectome Workbench but is needed for the full functionality of that program.
14 Feb 2018 diamond updated to version 0.9.9
DIAMOND is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity.
14 Feb 2018 ximmer updated to version 1.0-551-ga40e933
Ximmer is a tool designed to help users of targeted high throughput genomic sequencing data (such as exome data) to accurately detect copy number variants (CNVs). Ximmer is not a copy number detection tool itself. Rather, it is a framework for running and evaluating other copy number detection tools.
14 Feb 2018 VEP updated to version 91
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 Feb 2018 bamtools updated to version 2.5.1
BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.
12 Feb 2018 Caffe2 updated to version 0.8.1
Caffe2 aims to provide an easy and straightforward way for you to experiment with deep learning and leverage community contributions of new models and algorithms. You can bring your creations to scale using the power of GPUs in the cloud or to the masses on mobile with Caffe2's cross-platform libraries.
12 Feb 2018 SciTE updated to version 4.0.3
SciTE or SCIntilla based Text Editor is a cross-platform text editor. Lightweight and built for speed, it is designed mainly for source editing, and performs syntax highlighting and inline function reference for many different languages.
12 Feb 2018 HMMER updated to version 3.1b2
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called "profile hidden Markov models" (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models.
12 Feb 2018 TransDecoder updated to version 5.0.1
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
12 Feb 2018 bbtools updated to version 37.36
An extensive set of bioinformatics tools including bbmap (short read aligner), bbnorm (kmer based normalization), dedupe (deduplication and clustering of unaligned reads), reformat (formatting and trimming reads) and many more.
12 Feb 2018 xHLA updated to version 2017-10-04
The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. xHLA iteratively refines the mapping results at the amino acid level to achieve high typing accuracy for both class I and II HLA genes.
9 Feb 2018 strelka updated to version 2.7.1
Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.
8 Feb 2018 iSAAC updated to version
iSAAC is an ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (Isaac Variant Caller)
8 Feb 2018 STAR updated to version 2.5.4a
Spliced Transcripts Alignment to a Reference
8 Feb 2018 hisat updated to version 2.0.5
HISAT is a fast and sensitive spliced alignment program which uses Hierarchical Indexing for Spliced Alignment of Transcripts.
8 Feb 2018 IGVTools updated to version 2.3.98
IGVTools provides utilities for working with ascii file formats used by the Integrated Genome Viewer. The files can be sorted, tiled, indexed, and counted.
8 Feb 2018 IGV updated to version 2.4.8
The Integrative Genomics Viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
8 Feb 2018 transvar updated to version 2.3.4
TransVar is a versatile annotator for 3-way conversion and annotation among genomic characterization(s) of mutations and transcript-dependent annotation(s).
8 Feb 2018 graphviz updated to version 2.40
Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
5 Feb 2018 rDock updated to version 2013.1
The rDock platform is a suite of command-line tools for high-throughput docking and virtual screening.
5 Feb 2018 globus-cli updated to version 1.2.3
Globus command line interface
3 Feb 2018 bedtools updated to version 2.27.1
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.
2 Feb 2018 snakemake updated to version 4.5.1
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.
2 Feb 2018 Genome Browser updated to version 360
The Genome Browser Mirror Fragments at Helix Systems 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.
1 Feb 2018 cutadapt updated to version 1.15
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.
30 Jan 2018 GCC updated to version 7.3.0
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, and Go, as well as libraries for these languages (libstdc++, libgfortran,...)
30 Jan 2018 PSIPRED updated to version 4.0
PSIPRED is a simple and accurate secondary structure prediction method, incorporating two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST (Position Specific Iterated - BLAST).
30 Jan 2018 SMR updated to version 0.702
SMR integrates summary-level data from GWAS with data from expression quantitative trait locus (eQTL) studies to identify genes whose expression levels are associated with a complex trait because of pleiotropy. It implements methods to test for pleiotropic association between the expression level of a gene and a complex trait of interest using summary-level data from GWAS and expression quantitative trait loci (eQTL) studies (Zhu et al. 2016 Nat Genet).
30 Jan 2018 InterVar updated to version 2.0
In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published updated standards and guidelines for the clinical interpretation of sequence variants with respect to human diseases on the basis of 28 criteria. However, variability between individual interpreters can be extensive because of reasons such as the different understandings of these guidelines and the lack of standard algorithms for implementing them, yet computational tools for semi-automated variant interpretation are not available. To address these problems, InterVar implements these criteria to help human reviewers interpret the clinical significance of variants. InterVar can take a pre-annotated or VCF file as input and generate automated interpretation on 18 criteria.
29 Jan 2018 meme updated to version 4.12.0
MEME is used to discover motifs in groups of DNA/protein sequences or databases.
26 Jan 2018 automake updated to version 1.15.1
Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards.
26 Jan 2018 m4 updated to version 1.4.18
GNU M4 is an implementation of the traditional Unix macro processor.
26 Jan 2018 ImageMagick updated to version 7.0.7
ImageMagick is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats.
The ImageMagick tools are available by default (e.g. type 'convert') or use 'module load ImageMagick' to load the latest versions.
26 Jan 2018 Lmod updated to version 7.7.14
Lmod Environment Module system from TACC
26 Jan 2018 bismark updated to version 0.19.0
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.
25 Jan 2018 rail-rna updated to version 0.2.4b
Spliced RNA-Seq aligner designed to take advantage of data from multiple samples.
23 Jan 2018 libpng updated to version 1.6.34
libpng is the official PNG reference library. It supports almost all PNG features, is extensible, and has been extensively tested for over 20 years.
23 Jan 2018 links updated to version 1.8.5
Long Interval Nucleotide K-mer Scaffolder
23 Jan 2018 FFTW updated to version 3.3.7
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
23 Jan 2018 Phenix updated to version 1.13-2998
PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods.
22 Jan 2018 OpenMPI updated to version 3.0.0
OpenMPI is a popular implementation of Ethernet MPI with very active support and development.
22 Jan 2018 CUDA updated to version 9.0.176
CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).
22 Jan 2018 alleleCount updated to version 3.3.1
Calculates genotype frequencies of a SNPMatrix. This component tests each SNP for its Hardy-Weinberg equilibrium. If there are NA values, the frequencies of missing value per sample in the input file are calculated.
19 Jan 2018 Blast updated to version 2.7.1+
NCBI's famous sequence database searching program which compares a nucleotide or protein query sequence against all sequences in a database.
19 Jan 2018 google-cloud-sdk updated to version 185.0.0
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.
17 Jan 2018 bowtie2 updated to version 2.3.4
A version of bowtie that's particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes
17 Jan 2018 Intel Compiler Suite updated to version 2018.1.163
Intel Compiler Suite for Linux. Includes C/C++ and Fortran compilers. Also includes the Math Kernel Library, Integrated Performance Primitives and Thread Building Blocks.
17 Jan 2018 Tex updated to version 2017
Tex + Latex + associated packages for high-quality text formatting.
17 Jan 2018 bowtie updated to version 1.2.2
bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.
17 Jan 2018 exomiser updated to version 9.0.0
The Exomiser is a Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file.
17 Jan 2018 git updated to version 2.15.1
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.
16 Jan 2018 libtiff updated to version 4.0.7
This software provides support for the Tag Image File Format (TIFF), a widely used format for storing image data.
16 Jan 2018 Imaris updated to version 9.1
Imaris provides scientists with solutions for processing, visualizing and analyzing multi-dimensional microscopic images. It reads images in many of the most commonly used proprietary formats.
10 Jan 2018 frealix updated to version 1.1.0
Frealix is a program for the refinement of helical filament reconstructions from cryo electron micrographs. It is primarily used to process images of amyloid fibrils, though it has also been tested on TMV and actin filaments.
10 Jan 2018 mosdepth updated to version 0.2.0
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
9 Jan 2018 libevent updated to version 2.1.8
The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.
8 Jan 2018 ngscheckmate updated to version 1.0.0
NGSCheckMate validates nucleotide sequencing sample identity from fastq, BAM, or VCF files.
8 Jan 2018 freeglut updated to version 3.0.0
FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library.
8 Jan 2018 glew updated to version 2.1.0
The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform.
8 Jan 2018 tmux updated to version 2.6
tmux is a terminal multiplexer.
Type 'module load tmux' to load the module, then 'tmux --help'
8 Jan 2018 BEAST updated to version 2.4.7
BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences.
4 Jan 2018 hhsuite updated to version 3.0-beta.3
The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
4 Jan 2018 clinEff updated to version 1.0h
ClinEff is a professional version of the SnpEff and SnpSift packages, suitable for production in clincal labs. ClinEff combines the flexibility of multiple SnpEff/SnpSift commands with simplicity of running one program to perform all the annotations at once (i.e. in a single pass). It is highly customizable and can be taylored to specific pipeline needs in Clinical production environments.
3 Jan 2018 snpEff updated to version 4.3t
snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).
2 Jan 2018 mdtraj updated to version 1.9.1
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.
29 Dec 2017 rvgdt updated to version 1.0
The Rare-Variant Generalized Disequilibrium Test
29 Dec 2017 parallel updated to version 20171222
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
28 Dec 2017 msmc updated to version 1.0.1
Implementation of the multiple sequential markovian coalescent
28 Dec 2017 psmc updated to version 0.6.5
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
27 Dec 2017 Huygens updated to version 17.10.0-p4
Huygens is an image restoration, deconvolution, resolution and noise reduction. It can process images from all current optical microscopes, including wide-field, confocal, Nipkow (scanning disk confocal), multiple-photon, and 4Pi microscopes.
26 Dec 2017 Qt updated to version 5.10.0
Qt is a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms with little or no change in the underlying codebase, while still being a native application with native capabilities and speed.
26 Dec 2017 gdc-client updated to version 1.3.0
The GDC Data Transfer Tool provides an optimized method of transferring data to and from the GDC, and enables resumption of interrupted transfers.
Scientific Databases updated in last 3 months
For a full list of scientific databases available on the NIH HPC systems, see this page

Updated Database Format Location
24 Mar 2018Protein Data BankPDB/pdb/pdb
21 Mar 2018ViralBlast/fdb/blastdb/viral
20 Mar 2018MitoFasta/fdb/fastadb/mito.nt.fas
20 Mar 2018MitoFasta/fdb/fastadb/mito.aa.fas
20 Mar 2018NCBI Taxonomytaxonomy/fdb/taxonomy
20 Mar 2018MitoBlast/fdb/blastdb/mito.aa
18 Mar 201816S MicrobialBlast/fdb/blastdb/16SMicrobial
16 Mar 2018Rat Genome (Rattus norvegicus) rn4MySQLNIH mirror of UCSC Genome Browser
16 Mar 2018Drosophila genome (Drosophila melanogaster) fb5MySQLNIH mirror of UCSC genome browser
13 Mar 2018Refseq Other GenomicFasta/fdb/fastadb/ref.other.genomic.fas
13 Mar 2018Protein Data BankFasta/fdb/fastadb/pdb.nt.fas
13 Mar 2018NCBI ntFasta/fdb/fastadb/nt.fas
13 Mar 2018SwissProtFasta/fdb/fastadb/swissprot.aa.fas
13 Mar 2018Protein Data BankFasta/fdb/fastadb/pdb.aa.fas
13 Mar 2018NCBI nrFasta/fdb/fastadb/nr.aa.fas
11 Mar 2018Protein Data BankBlast/fdb/blastdb/pdbaa
11 Mar 2018SwissProtBlast/fdb/blastdb/swissprot
11 Mar 2018Protein Data BankBlast/fdb/blastdb/pdbnt
07 Mar 2018NCBI ntBlast/fdb/blastdb/nt
07 Mar 2018NCBI nrBlast/fdb/blastdb/nr
06 Mar 2018EST - othersBlast/fdb/blastdb/est_others
05 Mar 2018ViralBlast/fdb/blastdb/viral
19 Feb 2018ANNOVARANNOVAR/fdb/annovar/current
12 Feb 2018ceasAnnotations/fdb/CEAS
01 Feb 2018HTGsBlast/fdb/blastdb/htgs
09 Jan 2018TCGA DREAM SMC synthetic dataBAM/fdb/DREAM/SMC
04 Jan 2018Human Genome hg19dbNSFP/fdb/dbNSFP/
27 Dec 2017YeastBlast/fdb/blastdb/yeast.nt
27 Dec 2017YeastBlast/fdb/blastdb/yeast.aa
27 Dec 2017DrosophilaBlast/fdb/blastdb/drosoph.nt
27 Dec 2017DrosophilaBlast/fdb/blastdb/drosoph.aa