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
| 19 Mar 2019 | netOglyc updated to version 3.1d | NetOglyc produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. 19 Mar 2019 | bowtie2 updated to version 2.3.5 | 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 19 Mar 2019 | cutadapt updated to version 2.1 | 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. 19 Mar 2019 | vt updated to version 0.577 | vt is a variant tool set that discovers short variants from Next Generation Sequencing data. 19 Mar 2019 | nvchecker updated to version 1.4 | nvchecker (short for new version checker) is for checking if a new version of some software has been released. 19 Mar 2019 | ncbi-vdb updated to version 2.9.6 | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. 19 Mar 2019 | ncbi-ngs updated to version 2.9.6 | NCBI's NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing 19 Mar 2019 | sratoolkit updated to version 2.9.6 | The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format. 18 Mar 2019 | viennarna updated to version 2.4.11 | RNA Secondary Structure Prediction and Comparison 18 Mar 2019 | globus-cli updated to version 1.10.0 | Globus command line interface 18 Mar 2019 | BEAST updated to version 1.10.4,2.5.2 | BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences. 18 Mar 2019 | whippet updated to version 0.11 | Lightweight and Fast; RNA-seq quantification at the event-level 18 Mar 2019 | RELION updated to version 3.0.2 | 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. 14 Mar 2019 | salmon updated to version 0.13.0 | a tool for quantifying the expression of transcripts using RNA-seq data. 14 Mar 2019 | mosdepth updated to version 0.2.5 | Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. 11 Mar 2019 | fmriprep updated to version 1.3.1 | A Robust Preprocessing Pipeline for fMRI Data 11 Mar 2019 | genrich updated to version 0.5 | Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment. 11 Mar 2019 | CCP4 updated to version 7.0.071 | CCP4 is a suite of programs for protein crystallography and structural biology. 11 Mar 2019 | Maven updated to version 3.6.0 | 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. 6 Mar 2019 | UNet updated to version 20190225 | U-Net is an image segmentation tool. It relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization. 6 Mar 2019 | idep updated to version 0.81 | iDEP (integrated Differential Expression and Pathway analysis) is shiny application for analyzing RNA-seq data 5 Mar 2019 | speedseq updated to version 0.1.2-20180208-4e60002 | SpeedSeq is a genome analysis platform designed for rapid whole-genome variant detection and interpretation 1 Mar 2019 | quast updated to version 5.0.2 | QUAST stands for QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. The package includes the general QUAST tool for genome assemblies, MetaQUAST, the extension for metagenomic datasets, and Icarus, interactive visualizer for these tools. 1 Mar 2019 | nodejs updated to version 10.15.2 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 1 Mar 2019 | minimap2 updated to version 2.16 | 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). 27 Feb 2019 | qcat updated to version 1.0.1 | qcat is Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files. 27 Feb 2019 | 3DSlicer updated to version 4.10.1 | 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. 27 Feb 2019 | neovim updated to version 0.3.4 | Neovim is a refactor, and sometimes redactor, in the tradition of Vim (which itself derives from Stevie). It is not a rewrite but a continuation and extension of Vim. 26 Feb 2019 | parallel updated to version 201901222 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 26 Feb 2019 | AWS updated to version 1.16.111 | Command-line tools for Amazon Web Services. Use 'module load python; aws -help' to see the command-line help, or http://aws.amazon.com/cli/. 26 Feb 2019 | vsearch updated to version 2.11.0 | 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. 25 Feb 2019 | icgc-get updated to version 0.6.1 | icgc-get provides a unified interface to the many sources of data from the International Cancer Genome Consortium. 25 Feb 2019 | singularity updated to version 3.1.0 | 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. 22 Feb 2019 | angsd updated to version 0.925 | 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. 22 Feb 2019 | JAMM updated to version 1.0.7.5 | JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets. 21 Feb 2019 | deepmedic updated to version 0.7.1 | This project aims to offer easy access to Deep Learning for segmentation of structures of interest in biomedical 3D scans. It is a system that allows the easy creation of a 3D Convolutional Neural Network, which can be trained to detect and segment structures if corresponding ground truth labels are provided for training. The system processes NIFTI images, making its use straightforward for many biomedical tasks. 19 Feb 2019 | Octave updated to version 4.4.1 | 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. 19 Feb 2019 | texinfo updated to version 6.6 | Texinfo is the official documentation format of the GNU project 19 Feb 2019 | viral-ngs updated to version 1.22.1 | viral-ngs comprises a set of viral genomics analysis pipelines developed by the Broad Institute 15 Feb 2019 | score-client updated to version 1.6.1 | The Score client replaces the ICGC storage client. To interact with cloud repositories such as AWS and Collaboratory, you will require the Score Client 14 Feb 2019 | PRSice updated to version 2.1.7 | PRSice is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses. 14 Feb 2019 | Neuron updated to version 7.6.5 | NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties. 14 Feb 2019 | meme updated to version 5.0.1 | MEME is used to discover motifs in groups of DNA/protein sequences or databases. 14 Feb 2019 | Canu updated to version 1.8 | 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. 13 Feb 2019 | EGA updated to version 2.2.2 | A download client for the European Genome-phenome Archive (EGA). The EGA is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. 13 Feb 2019 | proseq updated to version 2.0 | proseq-2.0 is a pipeline for preprocesses and alignment of run-on sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing 13 Feb 2019 | google-cloud-sdk updated to version 234.0.0 | 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. 13 Feb 2019 | interproscan updated to version 5.33-72.0 | 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. 12 Feb 2019 | truffle updated to version 1.38 | "Fast and accurate shared segment detection and relatedness estimation in un- phased genetic data using TRUFFLE" 12 Feb 2019 | multiqc updated to version 1.7 | aggregates results for various frequently used bioinformatics tools across multiple samples into a nice visual report 11 Feb 2019 | iva updated to version 1.0.8 | IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth. 11 Feb 2019 | rclone updated to version 1.46 | 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. 10 Feb 2019 | Tybalt updated to version 20190214 | Tybalt implements a Variational EutoEncoder (VAE), a deep neural network approach capable of generating meaningful latent spaces for image and text data. Tybalt has been trained on The Cancer Genome Atlas (TCGA) pan-cancer RNA-seq data and used to identify specific patterns in the VAE encoded features. 8 Feb 2019 | TransDecoder updated to version 5.5.0 | 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. 8 Feb 2019 | uropa updated to version 2.0.3 | UROPA is a command line based tool for genomic region annotation 7 Feb 2019 | ctffind updated to version 4.1.13 | Programs for finding CTFs of electron micrographs 7 Feb 2019 | CutRunTools updated to version 20190204 | CutRunTools is a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CutRun primary cleavage data. CutRunTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CutRun. 6 Feb 2019 | mash updated to version 2.1 | mash is a command line tool and library to provide fast genome and metagenome distance estimation using MinHash. Only command line tool is installed 5 Feb 2019 | porechop updated to version 0.2.4 | Trim/demultiplex Oxford Nanopore reads 5 Feb 2019 | cromwell updated to version 36 | A Workflow Management System geared towards scientific workflows. 5 Feb 2019 | bali-phy updated to version 3.4.1 | BAli-Phy is MCMC software developed by Ben Redelings with Marc Suchard for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling via probabilistic programming. 5 Feb 2019 | delly updated to version 0.8.1 | 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. 4 Feb 2019 | seqtk updated to version 1.3 | seqtk is a toolkit for processing sequences in FASTA/Q formats 4 Feb 2019 | Ruby updated to version 2.6.1 | A dynamic, open source programming language with a focus on simplicity and productivity 4 Feb 2019 | flye updated to version 2.4 | Fast and accurate de novo assembler for single molecule sequencing reads 4 Feb 2019 | Julia updated to version 1.1.0 | high level, dynamic language for technical computing 4 Feb 2019 | GATK updated to version 4.1.0.0 | 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. 3 Feb 2019 | king updated to version 2.1.6 | 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. 1 Feb 2019 | OptiType updated to version 1.3.2 | OptiType is a HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. 31 Jan 2019 | seqan updated to version 2.4.0 | SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. This package also contains a suite of apps, including Fiona, Gustaf, Mason, RazerS 3, Yara, SeqAn T-Coffee, Stellar, and searchjoin. 30 Jan 2019 | kallisto updated to version 0.45.0 | kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. 30 Jan 2019 | sniffles updated to version 1.0.11 | Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. 30 Jan 2019 | mothur updated to version 1.41.3 | mothur is a tool for analyzing 16S rRNA gene sequences generated on multiple platforms as part of microbial ecology projects. 30 Jan 2019 | synapseclient updated to version 1.9.1 | The synapseclient package provides an interface to Synapse, a collaborative workspace for reproducible, data intensive research projects 29 Jan 2019 | telescope updated to version 1.0.2 | Single locus resolution of Transposable ELEment expression. Telescope estimates transposable element expression (retrotranscriptome) resolved to specific genomic locations. It directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model. 28 Jan 2019 | gffcompare updated to version 0.10.6 | gffcompare can be used to compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie). It can collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples) and classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format). 28 Jan 2019 | RAxML updated to version 8.2.12 | 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). 28 Jan 2019 | exonerate updated to version 2.4.0 | Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics. 28 Jan 2019 | RepeatMasker updated to version 4.0.8 | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. 28 Jan 2019 | xclip updated to version 0.13 | xclip is a command line utility that is designed to run on any system with an X11 implementation. It provides an interface to X selections ("the clipboard") from the command line. It can read data from standard in or a file and place it in an X selection for pasting into other X applications. xclip can also print an X selection to standard out, which can then be redirected to a file or another program. 25 Jan 2019 | turbovnc updated to version 2.2.1 | TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads. 25 Jan 2019 | purge_haplotigs updated to version 1.0.4 | purge_haplotigs is a pipeline to help with curating heterozygous diploid genome assemblies. 24 Jan 2019 | |