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 Apr 2021 | shapeit updated to version 4.2.1 | SHAPEIT is a fast and accurate haplotype inference software 19 Apr 2021 | mothur updated to version 1.45.2 | mothur is a tool for analyzing 16S rRNA gene sequences generated on multiple platforms as part of microbial ecology projects. 19 Apr 2021 | PyRosetta updated to version 279.py3.7 | PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions. 19 Apr 2021 | xpdf updated to version 4.03 | Xpdf is a free PDF viewer and toolkit, including a text extractor, image converter, HTML converter, and more. Most of the tools are available as open source. 18 Apr 2021 | PartekFlow updated to version 10.0.21.0411 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 16 Apr 2021 | SimNIBS updated to version 3.2.2 | 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). 15 Apr 2021 | R updated to version 4.0.5 | 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, ...). 15 Apr 2021 | minimap2 updated to version 2.18 | 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). 13 Apr 2021 | tmux updated to version 3.2 | tmux is a terminal multiplexer. Type 'module load tmux' to load the module, then 'tmux --help' 12 Apr 2021 | vsearch updated to version 2.16.0 | 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. 9 Apr 2021 | subread updated to version 2.0.2 | High-performance read alignment, quantification and mutation discovery 9 Apr 2021 | sicer updated to version 2-1.0.3 | A clustering approach for identification of enriched domains from histone modification ChIP-Seq data 8 Apr 2021 | symmetry updated to version 2.1.0 | This project collects tools to detect, analyze, and visualize protein symmetry. 8 Apr 2021 | bonito updated to version 0.3.6 | A PyTorch Basecaller for Oxford Nanopore Reads 6 Apr 2021 | IMOD updated to version 4.11.5 | 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. 6 Apr 2021 | PEET updated to version 1.15.0 | PEET (Particle Estimation for Electron Tomography) is an open-source package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. It seeks the optimal alignment of each particle against a reference volume through several iterations. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. 5 Apr 2021 | STAR updated to version 2.7.8a | Spliced Transcripts Alignment to a Reference 5 Apr 2021 | STAR-Fusion updated to version 1.10.0 | Transcript fusion detection 2 Apr 2021 | pangolin updated to version 2.3.6 | Phylogenetic Assignment of Named Global Outbreak LINeages. PANGOLIN is a system for identifying phylogenetic COVID lineages that contribute most to active spread. 2 Apr 2021 | lumpy updated to version 0.3.1 | A probabilistic framework for structural variant discovery. 2 Apr 2021 | cryolo updated to version 1.7.6.3 | Automated particle picker for cryo-EM 2 Apr 2021 | winnowmap updated to version 2.0 | winnowmap is used for mapping ONT and PacBio reads to repetitive reference sequences. 31 Mar 2021 | git updated to version 2.31.1 | 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. 30 Mar 2021 | fanc updated to version 0.9.17 | FAN-C is a toolkit for the analysis and visualization of Hi-C data. Beyond objects generated within FAN-C, the toolkit is largely compatible with Hi-C files from Cooler and Juicer. 30 Mar 2021 | fade updated to version 0.2.2 | Fragmentase Artifact Detection and Elimination 30 Mar 2021 | stringtie updated to version 2.1.5 | 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. 30 Mar 2021 | vcf2maf updated to version 1.6.20 | A smarter, more reproducible, and more configurable tool for converting a VCF to a MAF. 29 Mar 2021 | spades updated to version 3.15.2 | SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. 29 Mar 2021 | rnaseqc updated to version 2.4.2 | RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. 29 Mar 2021 | bwa-mem2 updated to version 2.2.1 | The next version of the bwa-mem algorithm in bwa. 29 Mar 2021 | VADR updated to version 1.1.3 | VADR stands for Viral Annotation DefineR. It is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families. It has been mainly tested for analysis of Norovirus, Dengue, and SARS-CoV-2 virus sequences in preparation for submission to the GenBank database. 26 Mar 2021 | iVar updated to version 1.3.1 | iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. 25 Mar 2021 | augustus updated to version 3.4.0 | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. 25 Mar 2021 | metabat updated to version 2.15 | MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data 25 Mar 2021 | abyss updated to version 2.3.0 | 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. 24 Mar 2021 | magetbrain updated to version 1.0 | Given a set of labelled MR images (atlases) and unlabelled images (subjects), MAGeT produces a segmentation for each subject using a multi-atlas voting procedure based on a template library made up of images from the subject set. 24 Mar 2021 | pandoc updated to version 2.13 | Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. 24 Mar 2021 | kronatools updated to version 2.8 | Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with any modern web browser. 24 Mar 2021 | ExpansionHunter updated to version 4.0.2 | Expansion Hunter: a tool for estimating repeat sizes. There are a number of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). Such repeat regions can expand to a size much larger than the read length and thereby cause a disease. Expansion Hunter aims to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat. 23 Mar 2021 | gdc-client updated to version 1.6.0 | The GDC Data Transfer Tool provides an optimized method of transferring data to and from the GDC, and enables resumption of interrupted transfers. 23 Mar 2021 | parallel updated to version 20210322 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 22 Mar 2021 | bpipe updated to version 0.9.10 | Bpipe provides a platform for running big bioinformatics jobs 22 Mar 2021 | gmap-gsnap updated to version 2021-03-08 | A Genomic Mapping and Alignment Programs 21 Mar 2021 | RepeatMasker updated to version 4.1.2 | 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. 21 Mar 2021 | rmblast updated to version 2.11.0 | 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. 19 Mar 2021 | minc-toolkit updated to version 1.9.18 | This metaproject bundles multiple MINC-based packages that historically have been developed somewhat independently 19 Mar 2021 | svtools updated to version 0.5.1 | Comprehensive utilities to explore structural variations in genomes 19 Mar 2021 | vireosnp updated to version 0.5.1 | Demultiplexing pooled scRNA-seq data without genotype reference 18 Mar 2021 | svtyper updated to version 0.7.1 | Svtyper is a Bayesian genotyper for structural variants. 18 Mar 2021 | mriqc updated to version 0.16.1 | MRIQC is an MRI quality control tool 18 Mar 2021 | PyMOL updated to version 2.4.0 | A comprehensive molecular visualization product for rendering and animating 3D molecular structures. 18 Mar 2021 | ncbi-vdb updated to version 2.11.0 | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. 18 Mar 2021 | ncbi-ngs updated to version 2.11.0 | NCBI's NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing 18 Mar 2021 | hisat updated to version 2.2.2.1-ngs2.11.0 | HISAT is a fast and sensitive spliced alignment program which uses Hierarchical Indexing for Spliced Alignment of Transcripts. 18 Mar 2021 | sratoolkit updated to version 2.11.0 | The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format. 18 Mar 2021 | Coot updated to version 0.9.5 | Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. 17 Mar 2021 | vg updated to version 1.31.0 | Tools for working with genome variation graphs 17 Mar 2021 | trinity updated to version 2.12.0 | 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. 16 Mar 2021 | tetoolkit updated to version 2.2.1 | A package for including transposable elements in differential enrichment analysis of sequencing datasets. 16 Mar 2021 | snakemake updated to version 6.0.5 | 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. 15 Mar 2021 | OpenBabel updated to version 3.1.1 | Open Babel is a chemical toolbox designed to speak the many languages of chemical data. 15 Mar 2021 | EMAN2 updated to version 2.91 | EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. 11 Mar 2021 | SAIGE updated to version 0.44.1 | R package for large-scale genetic association studies. 11 Mar 2021 | multiqc updated to version 1.10 | aggregates results for various frequently used bioinformatics tools across multiple samples into a nice visual report 10 Mar 2021 | RevBayes updated to version 1.1.1 | Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language 9 Mar 2021 | civet updated to version 2.1.1 | civet is a brain-imaging pipeline for analysis of large MR data sets. civet extracts and analyses cortical surfaces from MR images, as well as many other volumetric and corticometric functions. 9 Mar 2021 | ITK-SNAP updated to version 3.8.0 | ITK-SNAP is a tool for segmentation of 3D biomedical images. It requires a graphical connection to run on the cluster. 9 Mar 2021 | busco updated to version 5.0.0 | BUSCO completeness assessments employ sets of Benchmarking Universal Single-Copy Orthologs from OrthoDB (www.orthodb.org) to provide quantitative measures of the completeness of genome assemblies, annotated gene sets, and transcriptomes in terms of expected gene content. 8 Mar 2021 | protobuf updated to version 3.15.5 | Protocol buffers are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data. Think XML, but smaller, faster, and simpler. 8 Mar 2021 | RELION updated to version 3.1.2 | 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. 5 Mar 2021 | pvactools updated to version 2.0.1 | pVACtools is a cancer immunotherapy suite consisting of pVACseq, pVACfuse, pVACvector 5 Mar 2021 | IGVTools updated to version 2.9.2 | IGVTools provides utilities for working with ascii file formats used by the Integrated Genome Viewer. The files can be sorted, tiled, indexed, and counted. 5 Mar 2021 | IGV updated to version 2.9.2 | The Integrative Genomics Viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. 5 Mar 2021 | dynamo updated to version 1.15.14 | Dynamo is a software environment for subtomogram averaging of cryo-EM data. 4 Mar 2021 | pomoxis updated to version 0.3.4 | Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing. Notably tools are included for generating and analysing draft assemblies. Many of these tools are used by the research data analysis group at Oxford Nanopore Technologies. 4 Mar 2021 | biobambam2 updated to version 2.0.179-release-20201228191456 | Tools for early stage alignment file processing. 4 Mar 2021 | breseq updated to version 0.35.5 | 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). 4 Mar 2021 | mash updated to version 2.3 | mash is a command line tool and library to provide fast genome and metagenome distance estimation using MinHash. Only command line tool is installed 4 Mar 2021 | cpdf updated to version 2.3.2 | Coherent PDF tools 4 Mar 2021 | bcbio-nextgen updated to version 1.2.7 | Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis 3 Mar 2021 | GAMESS updated to version 30Sep20-R2 | GAMESS is a general ab initio quantum chemistry package. 3 Mar 2021 | dcm2niix updated to version 1.0.20201102 | DICOM to NIfTI converter 2 Mar 2021 | |