Application updates in the last 3 months
To see all versions available for any application, use module avail application_nameAll centrally-installed applications are listed on the Applications page
| Updated | Application
| 18 Aug 2017 | RELION updated to version 2.1-beta-1 | 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. 17 Aug 2017 | admixture updated to version 1.3.0 | ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. 17 Aug 2017 | lammps updated to version 31Mar17 | LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. It runs on a variety of different computer systems, including single processor systems, distributed-memory machines with MPI, and GPU and Xeon Phi systems. LAMMPS is open source software, released under the GNU General Public License. 16 Aug 2017 | taxtastic updated to version 0.7.1 | Build and maintain reference packages-- i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information. 16 Aug 2017 | svviz updated to version 1.6.1 | svviz visualizes high-throughput sequencing data relevant to a structural variant. Only reads supporting the variant or the reference allele will be shown. svviz can operate in both an interactive web browser view to closely inspect individual variants, or in batch mode, allowing multiple variants (annotated in a VCF file) to be analyzed simultaneously. 15 Aug 2017 | ctffind updated to version 4.1.8 | Programs for finding CTFs of electron micrographs 9 Aug 2017 | AfterQC updated to version 0.9.6 | Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. 9 Aug 2017 | minc-toolkit updated to version 1.9.15 | This metaproject bundles multiple MINC-based packages that historically have been developed somewhat independently 9 Aug 2017 | nextflow updated to version 0.25.5 | Data-driven computational pipelines 7 Aug 2017 | 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. 4 Aug 2017 | atropos updated to version 1.1.4 | An NGS read trimming tool that is specific, sensitive, and speedy. 3 Aug 2017 | crystfel updated to version 0.6.3 | 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. 3 Aug 2017 | adapterremoval updated to version 2.2.2 | rapid adapter trimming, identification, and read merging 3 Aug 2017 | varsim updated to version 0.8.1 | A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications 2 Aug 2017 | squid updated to version 1.0 | SQUID is designed to detect transcriptomic structural variations from RNA-seq alignment. 2 Aug 2017 | openjdk updated to version 1.8.0_121 | OpenJDK (Open Java Development Kit) is a free and open source implementation of the Java Platform, Standard Edition (Java SE). It is the official reference implementation of Java SE since version 7.[ 2 Aug 2017 | presto updated to version 0.5.4.999 | A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data. 2 Aug 2017 | THetA updated to version 0.7-7-g8f93e6c | Tumor Heterogeneity Analysis (THetA) is an algorithm used to estimate tumor purity and clonal/subclonal copy number aberrations simultaneously from high-throughput DNA sequencing data. 1 Aug 2017 | ldsc updated to version 1.0.0-92-gcf1707e | ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores. 1 Aug 2017 | dogpicker updated to version 0.2.1 | Particle picker that uses difference of Gaussians (DoG) for picking particles. 1 Aug 2017 | GATK updated to version 3.8-0 | 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. 1 Aug 2017 | Genome Browser updated to version 352 | 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. 31 Jul 2017 | magic updated to version b2103fd | A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data. 31 Jul 2017 | DEPICT updated to version 140721 | DEPICT is an integrative tool that based on predicted gene functions systematically prioritizes the most likely causal genes at associated loci, highlights enriched pathways, and identifies tissues/cell types where genes from associated loci are highly expressed 31 Jul 2017 | MAGMA updated to version 1.06 | MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis. 31 Jul 2017 | BOLT-LMM updated to version 2.2 | The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model (LMM) 31 Jul 2017 | smc++ updated to version 1.9.4 | SMC++ is a program for estimating the size history of populations from whole genome sequence data. 31 Jul 2017 | art updated to version 20160605 | ART is a set of simulation tools to generate synthetic next-generation sequencing reads. 29 Jul 2017 | fqtools updated to version 2.0 | Tools for manipulating fastq files 28 Jul 2017 | QIIME updated to version 2.2017.7 | 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). 28 Jul 2017 | SGA-ICE updated to version 20170728 | The script SGA-ICE (SGA-Iteratively Correcting Errors) implements iterative error correction by using modules from the String Graph Assembler (SGA). 26 Jul 2017 | ANNOVAR updated to version 2017-07-16 | ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. 26 Jul 2017 | EDirect updated to version 7.00 | Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. 26 Jul 2017 | PartekFlow updated to version 6.0.17.0723 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 26 Jul 2017 | pigz updated to version 2.3.4 | pigz (parallel implementation of gzip) is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. 25 Jul 2017 | Phenix updated to version 1.12-2829 | PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods. 24 Jul 2017 | gmap-gsnap updated to version 2017-06-20 | A Genomic Mapping and Alignment Programs 24 Jul 2017 | circos updated to version 0.69-5 | Circos is a program for the generation of publication-quality, circularly composited renditions of genomic data and related annotations. Circos is particularly suited for visualizing alignments, conservation and intra and inter-chromosomal relationships. Also, Circos is useful to visualize any type of information that benefits from a circular layout. Thus, although it has been designed for the field of genomics, it is sufficiently flexible to be used in other data domains. 24 Jul 2017 | plink updated to version 1.9.0-beta4.4 | PLINK is whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 21 Jul 2017 | pbsuite updated to version 15.8.24 | The PBSuite contains two projects created for analysis of Pacific Biosciences long-read sequencing data: PBHoney and PBJelly. PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants. PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. 20 Jul 2017 | oases updated to version 0.2.1 | oases is a de novo transcriptome assembler based on the Velvet genome assembler core. 20 Jul 2017 | rclone updated to version 1.36 | Rclone is a utility for synchronizing directories on a file-based storage system (e.g. /home or /data) with an object store such as Amazon S3. It uses the S3 protocol, and it can be used with the HPC object storage system. 19 Jul 2017 | Canu updated to version 1.5 | Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). Canu will correct the reads, then trim suspicious regions (such as remaining SMRTbell adapter), then assemble the corrected and cleaned reads into unitigs. 19 Jul 2017 | kplogo updated to version 1.1 | k-mer probability logo (kpLogo) is a probability-based logo tool for integrated detection and visualization of position-specific ultra-short motifs from a set of aligned sequences 18 Jul 2017 | R updated to version 3.4.0 | R (the R Project) is a language and environment for statistical computing and graphics. R is similar to S, and provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...). 18 Jul 2017 | multiqc updated to version 1.1 | aggregates results for various frequently used bioinformatics tools across multiple samples into a nice visual report 18 Jul 2017 | cutadapt updated to version 1.14 | 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. 18 Jul 2017 | snakemake updated to version 3.13.3 | 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. 18 Jul 2017 | trup updated to version 01062017 | TRUP is a Tumor-specimen suited RNA-seq Unified Pipeline 18 Jul 2017 | supernova updated to version 1.2.0 | Supernova generates highly-contiguous, phased, whole-genome de novo assemblies from a Chromium-prepared library. 17 Jul 2017 | caffe updated to version 1.0.0 | Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors. 17 Jul 2017 | Octave updated to version 4.0.3 | GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. 17 Jul 2017 | LAPACK updated to version 3.7.1 | LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. 15 Jul 2017 | basespace_cli updated to version 0.8.12 | Command line interface for Illumina's BaseSpace 13 Jul 2017 | nucleoatac updated to version 0.3.4 | package calling nucleosome positions and occupancy using ATAC-Seq data 13 Jul 2017 | rilseq updated to version 0.49 | RILseq computational protocol 13 Jul 2017 | penncnv updated to version 1.0.4 | kilobase-resolution detection of copy number variations (CNVs) from Illumina high-density SNP genotyping data 12 Jul 2017 | salmon updated to version 0.8.2 | a tool for quantifying the expression of transcripts using RNA-seq data. 12 Jul 2017 | dosageconvertor updated to version 1.0.4 | DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK. 12 Jul 2017 | vcftools updated to version 0.1.15 | 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. 12 Jul 2017 | 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. 11 Jul 2017 | delly updated to version 0.7.7 | 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. 11 Jul 2017 | bowtie2 updated to version 2.3.2 | 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 10 Jul 2017 | laser updated to version 2.04 | LASER is a program to estimate individual ancestry by directly analyzing shotgun sequence reads without calling genotypes. 10 Jul 2017 | mixcr updated to version 2.1.3 | MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data. 10 Jul 2017 | datamash updated to version 1.1.1 | datamash is a command-line program which performs basic numeric,textual and statistical operations on input textual data files. 10 Jul 2017 | IGVTools updated to version 2.3.94 | IGVTools provides utilities for working with ascii file formats used by the Integrated Genome Viewer. The files can be sorted, tiled, indexed, and counted. 10 Jul 2017 | IGV updated to version 2.3.94 | The Integrative Genomics Viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. 7 Jul 2017 | circleseq updated to version 1.0 | Circleseq takes sample-specific paired end FASTQ files as input and produces a list of CIRCLE-seq detected off-target cleavage sites as output. 7 Jul 2017 | Scipion updated to version 1.1 | 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. 6 Jul 2017 | samtools updated to version 1.5 | The samtools package now provides samtools, bcftools, tabix, and the underlying htslib library. 5 Jul 2017 | IMOD updated to version 4.9.4 | IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. 5 Jul 2017 | LongRanger updated to version 2.1.3 | Long Ranger is a set of analysis pipelines that processes GemCode sequencing output to align reads and call and phase SNPs, indels, and structural variants Loupe is a genome browser designed to visualize the Linked-Read data produced by the 10x Chromium Platform. 5 Jul 2017 | intervene updated to version 0.5.8 | a tool for intersection and visualization of multiple genomic region sets 5 Jul 2017 | Huygens updated to version 17.04.0-p6 | 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. 3 Jul 2017 | RSD updated to version 1.1.7 | Reciprocal Smallest Distance (RSD) is a pairwise orthology algorithm that uses global sequence alignment and maximum likelihood evolutionary distance between sequences to accurately detects orthologs between genomes. 30 Jun 2017 | Canvas updated to version 1.25 | Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data. 30 Jun 2017 | poretools updated to version 0.6.1a1 | Poretools is a toolkit for manipulating and exploring nanopore sequencing data sets. Poretools operates on individual FAST5 files, directory of FAST5 files, and tar archives of FAST5 files. 29 Jun 2017 | kilosort updated to version 8738ef7 | a Matlab-based program for identifying and sorting neuronal spikes from multi-channel electrophysiological recording data sets. 29 Jun 2017 | matlab-npy updated to version 524bd14 | read/write NumPy .NPY files in MATLAB 29 Jun 2017 | phy updated to version 1.0.9 | phy is an open source neurophysiological data analysis package in Python. It provides features for sorting, analyzing, and visualizing extracellular recordings made with high-density multielectrode arrays containing hundreds to thousands of recording sites. 28 Jun 2017 | OpenCV updated to version 3.2.0 | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. 27 Jun 2017 | |