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
| 2 Jun 2020 | xcpengine updated to version 1.2.1 | xpcEngine performs denoising and estimation of Functional Connectivity on fMRI datasets 2 Jun 2020 | rilseq updated to version 0.75 | RILseq computational protocol 2 Jun 2020 | PRSice updated to version 2.3.1 | PRSice is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses. 1 Jun 2020 | fusioninspector updated to version 2.3.0 | In silico Validation of Fusion Transcript Predictions 1 Jun 2020 | HMMRATAC updated to version 1.2.10 | HMMRATAC peak caller for ATAC-seq data 1 Jun 2020 | Hail updated to version 0.2.43 | Hail is an open-source, scalable framework for exploring and analyzing genomic data. 1 Jun 2020 | stringtie updated to version 2.0.3b | 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. 1 Jun 2020 | vscode updated to version 1.45.1 | Free source code editor with many utilities for Python, Julia and others. 1 Jun 2020 | cutadapt updated to version 2.10 | 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. 1 Jun 2020 | nvchecker updated to version 1.6 | nvchecker (short for new version checker) is for checking if a new version of some software has been released. 31 May 2020 | nodejs updated to version 12.17.0 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 28 May 2020 | mrtrix updated to version 3.0.0 | MRtrix provides a large suite of tools for image processing, analysis and visualisation, with a focus on the analysis of white matter using diffusion-weighted MRI. 28 May 2020 | VEP updated to version 100.2 | 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. 28 May 2020 | ChIPseeqer updated to version 2.1 | ChIPseeqer is an integrative, comprehensive, fast and user-friendly computational framework for in-depth analysis of ChIP-seq datasets. It combinse several computational tools in order to create easily customized workflows that can be adapted to the user’s needs and objectives. 28 May 2020 | TelomereHunter updated to version 1.1.0 | TelomereHunter is a software for the detailed characterization of telomere maintenance mechanism footprints in the genome. The tool is implemented for the analysis of large cancer genome cohorts and provides a variety of diagnostic diagrams as well as machine-readable output for subsequent analysis. 28 May 2020 | sratoolkit updated to version 2.10.7 | The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format. 26 May 2020 | rscape updated to version 1.5.2 | RNA Significant Covariation Above Phylogenetic Expectation is a program that given a multiple sequence alignment of RNA sequences 26 May 2020 | boost updated to version 1.73 | 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. 22 May 2020 | Freesurfer updated to version 7.1.0 | Freesurfer is a set of automated tools for reconstruction of the brain's cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface. 21 May 2020 | EVcouplings updated to version 0.0.5 | Helps to predict protein structure, function and mutations using evolutionary sequence covariation. 21 May 2020 | intarna updated to version 3.2.0 | IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. 21 May 2020 | rnaview updated to version current | The RNAView program generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions. 21 May 2020 | rnastructure updated to version 6.2 | RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. 20 May 2020 | vcflib updated to version 1.0.1 | a simple C++ library for parsing and manipulating VCF files, + many command-line utilities 20 May 2020 | slamdunk updated to version 0.4.3 | SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis. 18 May 2020 | PyCharm updated to version 2018.3.5 | A Python IDE 18 May 2020 | nanopolish updated to version 0.13.2 | 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). 15 May 2020 | gen3-client updated to version 2020.05 | The gen3-client provides an easy-to-use, command-line interface for uploading and downloading data files to and from a Gen3 data commons from the terminal or command prompt. 14 May 2020 | fusioncatcher updated to version 1.20 | 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. 14 May 2020 | samtools updated to version 1.10 | The samtools package now provides samtools, bcftools, tabix, and the underlying htslib library. 14 May 2020 | crystfel updated to version 0.9.0.5ae3043d | 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. 14 May 2020 | PartekFlow updated to version 9.0.20.0510 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 13 May 2020 | tvb updated to version 1.5.8 | 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 13 May 2020 | GATK updated to version 4.1.7.0 | 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. 13 May 2020 | AMON updated to version 1.0.0 | AMON (Annotation of Metabolite Origins via Networks) is an open-source bioinformatics application that can be used to (1) annotate which compounds in the metabolome could have been produced by bacteria present or the host; (2) evaluate the pathway enrichment of host verses microbial metabolites, and (3) to visualize which compounds may have been produced by host versus microbial enzymes in KEGG pathway maps. 11 May 2020 | spm12 updated to version r7771 | The (S)tatistical (P)ara(M)etric application analyzes brain imaging data. 11 May 2020 | Rosetta updated to version 2020.11 | 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... 8 May 2020 | QTLtools updated to version 1.2 | A tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps. 6 May 2020 | lafter updated to version 1.1 | LAFTER is a local filter for single particle TEM reconstructions. 5 May 2020 | Phenix updated to version 1.18-3855 | PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods. 5 May 2020 | MySQL updated to version 8.0.20 | MySQL is an open-source relational database management system. 5 May 2020 | MIPAV updated to version 10.0.0 | The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. 5 May 2020 | m2clust updated to version 0.0.8 | m2clust provides an elegant clustering approach to find clusters in data sets with different density and resolution. 4 May 2020 | netpbm updated to version 10.86.12 | Netpbm is a toolkit for manipulation of graphic images, including conversion of images between a variety of different formats. There are over 300 separate tools in the package including converters for about 100 graphics formats. Examples of the sort of image manipulation we're talking about are: Shrinking an image by 10%; Cutting the top half off of an image; Making a mirror image; Creating a sequence of images that fade from one image to another. 1 May 2020 | taiji updated to version v1.2.0 | The Taiji software is a versatile genomics data analysis pipeline. It can be used to analyze ATAC-seq, RNA-seq, single cell ATAC-seq and Drop-seq data. 1 May 2020 | GEMMA updated to version 0.98.1 | GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS). 30 Apr 2020 | bbtools updated to version 38.82 | 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. 30 Apr 2020 | angsd updated to version 0.930 | ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data. The software is written in C++ and has been used on large sample sizes. 29 Apr 2020 | hyphy updated to version 2.5.11 | 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. 29 Apr 2020 | abyss updated to version 2.2.4 | Abyss represents Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. The parallel version is implemented using MPI and is capable of assembling larger genomes. 29 Apr 2020 | globus_sdk updated to version 1.9.0 | Pythonic interface to Globus REST APIs, including the Transfer API and the Globus Auth API 29 Apr 2020 | MotionCor2 updated to version 1.3.1 | 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. 29 Apr 2020 | mothur updated to version 1.44.1 | mothur is a tool for analyzing 16S rRNA gene sequences generated on multiple platforms as part of microbial ecology projects. 28 Apr 2020 | BRASS updated to version 6.3.1 | BRASS analyses one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints. 28 Apr 2020 | cmdstan updated to version 2.23.0 | Command line interface to stan 27 Apr 2020 | diamond updated to version 0.9.32 | 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. 27 Apr 2020 | infernal updated to version 1.1.3 | Package for searching DNA sequence databases for RNA structure and sequence similarities 24 Apr 2020 | chipseq_pipeline updated to version 1.4.0.1 | AQUAS Transcription Factor and Histone ChIP-Seq processing pipeline. The AQUAS pipeline is based off the ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline specifications (by Anshul Kundaje) 24 Apr 2020 | Scramble updated to version 0.0.20190211.82c78b9 | Scramble is a mobile element insertion (MEI) detection tool. It identifies clusters of soft clipped reads in a BAM file, builds consensus sequences, aligns to representative L1Ta, AluYa5, and SVA-E sequences, and outputs MEI calls. 23 Apr 2020 | epic2 updated to version 0.0.41 | Chip-Seq broad peak/domain finder based on SICER 22 Apr 2020 | vireosnp updated to version 0.3.2 | Demultiplexing pooled scRNA-seq data without genotype reference 22 Apr 2020 | seqkit updated to version 0.12.1 | A cross-platform toolkit for FASTA/Q file manipulation 22 Apr 2020 | cellsnp updated to version 0.1.7 | Pileup biallelic SNPs from single-cell and bulk RNA-seq data 22 Apr 2020 | salmon updated to version 1.2.0 | a tool for quantifying the expression of transcripts using RNA-seq data. 21 Apr 2020 | igblast updated to version 1.16.0 | IgBlast is a sequence analysis tool for immunoglobulin variable domains. 21 Apr 2020 | IGVTools updated to version 2.8.2 | IGVTools provides utilities for working with ascii file formats used by the Integrated Genome Viewer. The files can be sorted, tiled, indexed, and counted. 21 Apr 2020 | sickle updated to version 1.33 | A windowed adaptive trimming tool for FASTQ files using quality 21 Apr 2020 | git updated to version 2.26.2 | 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 Apr 2020 | vcf2maf updated to version 1.6.18 | A smarter, more reproducible, and more configurable tool for converting a VCF to a MAF. 17 Apr 2020 | kaiju updated to version 1.7.3 | Kaiju is a program for the taxonomic classification of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. 16 Apr 2020 | deepvariant updated to version 0.10.0 | DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. 16 Apr 2020 | rmblast updated to version 2.10.0 | RMBlast is a RepeatMasker-compatible version of the standard NCBI blastn program. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. 16 Apr 2020 | IGV updated to version 2.8.2 | The Integrative Genomics Viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. 16 Apr 2020 | mixcr updated to version 3.0.13 | MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data. 16 Apr 2020 | medaka updated to version 0.12.1 | 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. 15 Apr 2020 | google-cloud-sdk updated to version 289.0.0 | 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. 14 Apr 2020 | fastq_screen updated to version 0.14.0 | FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. 14 Apr 2020 | csvkit updated to version 1.0.5 | csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. 14 Apr 2020 | TaxonKit updated to version 0.5.0 | A Cross-platform and Efficient NCBI Taxonomy Toolkit 14 Apr 2020 | tantan updated to version 22 | A tool to mask low complexity and short period tandem repeats 14 Apr 2020 | Genome Browser updated to version 396 | 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. 14 Apr 2020 | Schrodinger updated to version 2020.1 | 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. 13 Apr 2020 | |