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
| 31 Mar 2020 | lefse updated to version 1.0.8 | LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance. 31 Mar 2020 | snakemake updated to version 5.13.0 | 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. 31 Mar 2020 | salmon updated to version 1.1.0 | a tool for quantifying the expression of transcripts using RNA-seq data. 31 Mar 2020 | Mathematica updated to version 12.1 | Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language. 31 Mar 2020 | Matlab updated to version 2020a | MATLAB is an interactive software package for scientific and engineering numeric computation. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an environment where problems and solutions are expressed just as they are written mathematically. 31 Mar 2020 | cpdf updated to version 2.3.1 | Coherent PDF tools 31 Mar 2020 | pandoc updated to version 2.9.2.1 | Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. 31 Mar 2020 | picard updated to version 2.22.2 | 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. 30 Mar 2020 | R updated to version 3.6.3 | 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, ...). 30 Mar 2020 | breseq updated to version 0.35.1 | breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data. It is intended for haploid microbial genomes (<20 Mb). 30 Mar 2020 | htseq updated to version 0.11.4 | HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. 30 Mar 2020 | humann2 updated to version 2.8.1 | HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). 27 Mar 2020 | screen updated to version 4.01 | Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells. 27 Mar 2020 | nanopolish updated to version 0.12.5 | 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). 27 Mar 2020 | vg updated to version 1.21.0 | Tools for working with genome variation graphs 27 Mar 2020 | ricopili updated to version 2019_Jun_25.001 | RICOPILI stands for Rapid Imputation and COmputational PIpeLIne for GWAS. 27 Mar 2020 | peddy updated to version 0.4.6 | peddy is used to compare sex and familial relationships given in a PED file with those inferred from a VCF file 26 Mar 2020 | pychopper updated to version 2.3.1 | Pychopper v2 is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads. 26 Mar 2020 | binlorry updated to version 1.3.1 | BinLorry is a tool for binning and filtering sequencing reads into distinct files. Reads can be binned and filtered by any attributes encoded in their headers, documented in a CSV file or by length. 26 Mar 2020 | cellxgene updated to version 0.15.0 | cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas. 26 Mar 2020 | MAJIQ updated to version 2.1-patched | Modeling Alternative Junction Inclusion Quantification. MAJIQ and Voila are two software packages that together define, quantify, and visualize local splicing variations (LSV) from RNA-Seq data. 26 Mar 2020 | cutadapt updated to version 2.9 | 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. 26 Mar 2020 | GATK updated to version 4.1.6.0 | 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. 26 Mar 2020 | mothur updated to version 1.44.0 | mothur is a tool for analyzing 16S rRNA gene sequences generated on multiple platforms as part of microbial ecology projects. 26 Mar 2020 | globus-cli updated to version 1.12.0 | Globus command line interface 26 Mar 2020 | golang updated to version 1.14.1 | The Go programming language 26 Mar 2020 | nextflow updated to version 20.01.0 | Data-driven computational pipelines 26 Mar 2020 | Julia updated to version 1.4.0 | high level, dynamic language for technical computing 25 Mar 2020 | gvcfgenotyper updated to version 2019.02.26 | A utility for merging and genotyping Illumina-style GVCFs. 24 Mar 2020 | bali-phy updated to version 3.5 | 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. 24 Mar 2020 | rseqc updated to version 3.0.1 | Rseqc comprehensively evaluate RNA-seq datasets generated from clinical tissues or other well annotated organisms such as mouse, fly and yeast. 24 Mar 2020 | fastqc updated to version 0.11.9 | It provide quality control functions to next gen sequencing data. 24 Mar 2020 | subread updated to version 2.0.0 | High-performance read alignment, quantification and mutation discovery 24 Mar 2020 | VarScan updated to version 2.4.3 | A platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. 24 Mar 2020 | viennarna updated to version 2.4.14 | RNA Secondary Structure Prediction and Comparison 23 Mar 2020 | CSD updated to version 2020 | The Cambridge Structural Database is the world repository of small molecule crystal structures. 23 Mar 2020 | fmriprep updated to version 20.0.5 | A Robust Preprocessing Pipeline for fMRI Data 23 Mar 2020 | cmdstan updated to version 2.21.0 | Command line interface to stan 20 Mar 2020 | flye updated to version 2.7 | Fast and accurate de novo assembler for single molecule sequencing reads 20 Mar 2020 | bowtie2 updated to version 2.4.1 | 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 20 Mar 2020 | deepvariant updated to version 0.9.0 | DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. 20 Mar 2020 | MCL updated to version 14-137 | MCL implements Markov cluster algorithm. Among its applications is the assignment of proteins into families based on precomputed sequence similarity information. This approach does not suffer from the problems that normally hinder other protein sequence clustering algorithms, such as the presence of multi-domain proteins, promiscuous domains and fragmented proteins. 20 Mar 2020 | SOAPdenovo-Trans updated to version 1.04 | SOAPdenovo-Trans is a de novo transcriptome assembler designed specifically for RNA-Seq. Its performance on transcriptome datasets from rice and mouse. It provides higher contiguity, lower redundancy and faster execution than other popular transcriptome assemblers. 20 Mar 2020 | kallisto updated to version 0.46.2 | 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. 19 Mar 2020 | rilseq updated to version 0.74 | RILseq computational protocol 19 Mar 2020 | LongRanger updated to version 2.2.2 | 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. 19 Mar 2020 | genometools updated to version 1.6.1 | collection of bioinformatic tools 19 Mar 2020 | shapeit updated to version 4.1.3 | SHAPEIT is a fast and accurate haplotype inference software 19 Mar 2020 | QIIME updated to version 2-2020.2 | 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). 19 Mar 2020 | OpenSlide updated to version 3.4.1 | OpenSlide is a C library for reading and manipulating digital slides of diverse vendor formats. It provides a simple interface to read whole-slide images (also known as virtual slides). OpenSlide has been used in the digital pathology projects. 19 Mar 2020 | BEAST updated to version 1.10.4,2.6.2 | BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences. 19 Mar 2020 | Huygens updated to version 19.10 | 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. 18 Mar 2020 | Canu updated to version 2.0 | 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. 18 Mar 2020 | ChromHMM updated to version 1.20 | ChromHMM is software for learning and characterizing chromatin states. 17 Mar 2020 | tandemtools updated to version current | Tool for assessing/improving assembly quality in extra-long tandem repeats 17 Mar 2020 | deeptools updated to version 3.4.1 | deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from deep-sequencing DNA sequencing experiments. 13 Mar 2020 | PyMOL updated to version 2.3.0 | A comprehensive molecular visualization product for rendering and animating 3D molecular structures. 13 Mar 2020 | OpenBabel updated to version 3.0.0 | Open Babel is a chemical toolbox designed to speak the many languages of chemical data. 10 Mar 2020 | HTGTSrep updated to version 9fe74ff | A pipeline for comprehensive analysis of HTGTS-Rep-seq. 10 Mar 2020 | m2clust updated to version 0.0.7 | m2clust provides an elegant clustering approach to find clusters in data sets with different density and resolution. 6 Mar 2020 | git updated to version 2.25.1 | 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. 4 Mar 2020 | GimmeMotifs updated to version 0.14.3 | GimmeMotifs is a pipeline for transcription factor motif analysis written in Python. It incorporates an ensemble of computational tools to predict motifs de novo from ChIP-sequencing data. Similar redundant motifs are compared using the weighted information content similarity score and clustered using an iterative procedure. A comprehensive output report is generated with several different evaluation metrics to compare and evaluate the results. 3 Mar 2020 | varsim updated to version 0.8.5 | A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications 2 Mar 2020 | raxml-ng updated to version 0.9.0 | RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Successor to raxml. 2 Mar 2020 | plink updated to version 2.3-alpha | PLINK is whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 26 Feb 2020 | hisat updated to version 2.2.1.0-sra2.10.4 | HISAT is a fast and sensitive spliced alignment program which uses Hierarchical Indexing for Spliced Alignment of Transcripts. 26 Feb 2020 | sratoolkit updated to version 2.10.4 | The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format. 26 Feb 2020 | ncbi-vdb updated to version 2.10.4 | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. 26 Feb 2020 | ncbi-ngs updated to version 2.10.4 | NCBI's NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing 26 Feb 2020 | vasttools updated to version 2.3.0 | A toolset for profiling alternative splicing events in RNA-Seq data. 25 Feb 2020 | SimNIBS updated to version 3.1.1 | SimNIBS is a free software package for the Simulation of Non-invasive Brain Stimulation. It allows for realistic calculations of the electric field induced by transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS). 25 Feb 2020 | DeepLabCut updated to version 2.1 | DeepLabCut is an open source toolbox that builds on a state-of-the-art human pose estimation algorithm. It allows training of a deep neural network by using limited training data to precisely track user-defined features, so that the human labeling accuracy will be matched. 25 Feb 2020 | htgts updated to version 2 | High-Throughput Genome-Wide Translocation Sequencing pipeline 25 Feb 2020 | uropa updated to version 3.5.0 | UROPA is a command line based tool for genomic region annotation 24 Feb 2020 | sysbench updated to version 1.0.11 | sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT. It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex workloads that do not involve a database server. 24 Feb 2020 | PRSice updated to version 2.2.12 | PRSice is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses. 24 Feb 2020 | TORTOISE updated to version 3.2.0 | (Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble) The TORTOISE software package is for processing diffusion MRI data. 24 Feb 2020 | boost updated to version 1.72 | 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. 24 Feb 2020 | parallel updated to version 20200222 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 20 Feb 2020 | DNAnexus updated to version 0.290.1 | DNAnexus is a cloud-based commercial solution for next-generation sequence analysis and visualization. It has a command-line interface (CLI) which can be used to log in to the DNAnexus platform, upload and navigate data, and launch analyses. 20 Feb 2020 | YOLO updated to version 20200211 | YOLO is a new approach to object detection. Prior work on object detection repurposed classifiers to perform detection. Instead, YOLO frames object detection as a regression problem to spatially separated bounding boxes and associated class probabilities. 20 Feb 2020 | AdmixTools updated to version 6.0 | ADMIXTOOLS is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. 20 Feb 2020 | |