| Updated | Application
| 24 Jul 2024 | LAST updated to version 1550 | LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially geared toward:
24 Jul 2024 | kallisto updated to version 0.51.0 | 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. 24 Jul 2024 | EDirect updated to version 22.4.20240723 | 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. 23 Jul 2024 | 3DSlicer updated to version 5.6.2 | 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. 23 Jul 2024 | stripy-pipeline updated to version 2.5 | STRipy-pipeline is non-graphical command-line version of STRipy that can be integrated into pipelines and analyse multiple STR or VNTR loci in parallel. 22 Jul 2024 | lz4 updated to version 1.10.0 | LZ4 is lossless compression algorithm, providing compression speed > 500 MB/s per core, scalable with multi-cores CPU. It features an extremely fast decoder, with speed in multiple GB/s per core, typically reaching RAM speed limits on multi-core systems. 22 Jul 2024 | SciTE updated to version 5.5.1 | SciTE or SCIntilla based Text Editor is a cross-platform text editor. Lightweight and built for speed, it is designed mainly for source editing, and performs syntax highlighting and inline function reference for many different languages. 22 Jul 2024 | CCP4 updated to version 9.0.001 | CCP4 is a suite of programs for protein crystallography and structural biology. 21 Jul 2024 | parallel updated to version 20240722 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 21 Jul 2024 | PartekFlow updated to version 12.0.1 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 18 Jul 2024 | DNAnexus updated to version 0.379.0 | 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. 18 Jul 2024 | synapseclient updated to version 4.4.0 | The synapseclient package provides an interface to Synapse, a collaborative workspace for reproducible, data intensive research projects 18 Jul 2024 | iqtree updated to version 2.3.5 | Efficient phylogenomic software by maximum likelihood 17 Jul 2024 | trgt updated to version 1.1.0 | TRGT is a tool for targeted genotyping of tandem repeats from PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence composition, mosaicism, and CpG methylation of each analyzed repeat. TRGT comes with a companion tool TRVZ for visualization of reads overlapping the repeats. 16 Jul 2024 | QIIME updated to version 2024.5 | 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). 16 Jul 2024 | VEP updated to version 112 | 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. 15 Jul 2024 | gnomix updated to version 0-20240703 | G-Nomix does high resolution ancestry deconvolution for high-throughput sequencing data. 12 Jul 2024 | parsnp updated to version 2.0.5 | Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees 11 Jul 2024 | kilosort4 updated to version 4.0.3 | Kilosort is a state-of-the-art neural signal processing algorithm designed for the analysis of large-scale neural recordings. It excels in sorting spikes in high-density multielectrode array recordings, making it an essential tool for neuroscientists. 9 Jul 2024 | tandem-genotypes updated to version 1.9.2 | tandem-genotypes finds changes in length of tandem repeats, from "long" DNA reads aligned to a genome. 9 Jul 2024 | nvchecker updated to version 2.15.1 | nvchecker (short for new version checker) is for checking if a new version of some software has been released. 9 Jul 2024 | nodejs updated to version 20.15.1 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 9 Jul 2024 | sniffles updated to version 2.4 | 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. 9 Jul 2024 | KrakenUniq updated to version 1.0.4 | KrakenUniq is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It combines the fast k-mer-based classification of Kraken (Wood and Salzberg, Genome Biology 2014) with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. 8 Jul 2024 | singularity updated to version 4.0.3 | 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. 3 Jul 2024 | stow updated to version 2.4.0 | GNU Stow is a symlink farm manager which takes distinct packages of software and/or data located in separate directories on the filesystem, and makes them appear to be installed in the same place. 3 Jul 2024 | tapestry updated to version 1.0.1 | Tapestry is a tool to validate and edit small eukaryotic genome assemblies using long sequence reads. It is designed to help identify complete chromosomes, symbionts, haplotypes, complex features and errors in close-to-complete genome assemblies. 1 Jul 2024 | vembrane updated to version 1.0.5 | Variant filtering using python expressions 1 Jul 2024 | spaceranger updated to version 3.0.1 | 10x pipeline for processing Visium spatial RNA-seq data 1 Jul 2024 | cryolo updated to version 1.9.9 | Automated particle picker for cryo-EM 28 Jun 2024 | Perl updated to version 5.40 | Perl is a highly capable, feature-rich programming language with over 30 years of development. 27 Jun 2024 | mafft updated to version 7.526 | Multiple alignment program for amino acid or nucleotide sequences 27 Jun 2024 | Phenix updated to version 1.21.1-5286 | PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods. 27 Jun 2024 | picard updated to version 3.2.0 | 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. 27 Jun 2024 | Genome Browser updated to version 466 | 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. 27 Jun 2024 | suppa updated to version 2.4 | Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions 27 Jun 2024 | SCENIC-plus updated to version 1.0a1 | SCENIC+ is a new method for the inference of enhancer-driven gene regulatory networks (eGRN). It predicts genomic enhancers along with candidate upstream transcription factors (TF) and links these enhancers to candidate target genes. Specific TFs for each cell type or cell state are predicted based on the concordance of TF binding site accessibility, TF expression, and target gene expression. 27 Jun 2024 | niftyreg updated to version 1.3.9 | NiftyReg is an open-source software for efficient medical image registration. It has been mainly developed by members of the Centre for Medical Image Computing at University College London, UK. 26 Jun 2024 | pymc updated to version 5.16.1 | PyMC is a probabilistic programming library for Python that allows users to build Bayesian models with a simple Python API and fit them using Markov chain Monte Carlo (MCMC) methods. 26 Jun 2024 | drop updated to version 1.4.0 | A pipeline to find aberrant events in RNA-Seq data. 26 Jun 2024 | fastq-pair updated to version 1.0 | Fastq-pair rewrites paired end fastq files to make sure that all reads have a mate and to separate out singletons. 26 Jun 2024 | omeropy updated to version 5.19.3 | OMERO.py provides Python bindings to the OMERO.blitz server as well as a pluggable command-line interface. ezomero is module with convenience functions for writing Python code that interacts with OMERO. 26 Jun 2024 | espresso updated to version 1.4.0 | ESPRESSO is a novel method for processing alignment of long read RNA-seq data, which can effectively improve splice junction accuracy and isoform quantification. ESPRESSO jointly considers alignments of all long reads aligned to a gene and uses error profiles of individual reads to improve the identification of splice junctions and the discovery of their corresponding transcript isoforms. 25 Jun 2024 | membrain-seg updated to version 0.0.2 | 3D membrane segmentation for cryo-electron tomography. 24 Jun 2024 | R updated to version 4.4.1 | 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, ...). 24 Jun 2024 | modkit updated to version 0.3.1 | A bioinformatics tool for working with modified bases from Oxford Nanopore. Specifically for converting modBAM to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics. 21 Jun 2024 | mono updated to version 6.12.0.199 | 21 Jun 2024 | dorado updated to version 0.7.2 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 18 Jun 2024 | plink updated to version 6-alpha | PLINK is whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 18 Jun 2024 | globus-cli updated to version 3.28.3 | Globus command line interface 18 Jun 2024 | jupyter updated to version 5.7.2 | Jupyter is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, machine learning and much more. 18 Jun 2024 | gthumb updated to version 3.12.0 | gThumb is an image viewer and browser 17 Jun 2024 | Acemd updated to version 3.7.3 | ACEMD is a high performance molecular dynamics code for biomolecular systems designed specifically for NVIDIA GPUs. Simple and fast, ACEMD uses very similar commands and input files of NAMD and output files as NAMD or Gromacs. 17 Jun 2024 | rclone updated to version 1.67.0 | 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. 17 Jun 2024 | arcashla updated to version 0.6.0 | high resolution HLA typing from RNA seq 13 Jun 2024 | cnvkit updated to version 0.9.11 | Copy number variant detection from targeted DNA sequencing 13 Jun 2024 | csvkit updated to version 2.0.0 | csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. 13 Jun 2024 | deeptools updated to version 3.5.5 | deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from deep-sequencing DNA sequencing experiments. 13 Jun 2024 | hwatch updated to version 0.3.10 | A modern alternative to the watch command, records the differences in execution results and can check these differences later. 13 Jun 2024 | cactus updated to version 2.8.2 | Cactus is a reference-free whole-genome multiple alignment program. 12 Jun 2024 | Rstudio updated to version 2024.04.2-764 | RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. 11 Jun 2024 | Xplor-NIH updated to version 3.9 | Xplor-NIH is a structure determination program which builds on the X-PLOR v3.851 program, including additional tools developed at the NIH. 11 Jun 2024 | vcf2maf updated to version 1.6.22 | A smarter, more reproducible, and more configurable tool for converting a VCF to a MAF. 11 Jun 2024 | gnuplot updated to version 6.0.1 | Gnuplot is a portable command-line driven graphing utility to visualize mathematical functions and data interactively, and can support many non-interactive uses such as web scripting. Type 'gnuplot' to run, or 'module avail gnuplot' to see other available versions. 11 Jun 2024 | mpich updated to version 4.2.1 | MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (both MPI-1 and MPI-2). 10 Jun 2024 | htseq updated to version 2.0.7 | HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. 10 Jun 2024 | fanc updated to version 0.9.28 | 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. 10 Jun 2024 | apptainer updated to version 1.3.2 | Apptainer allows you to build and run Linux containers with emphasis on use in HPC. Apptainer is the Linux Foundation variant of and successor to the widely popular Singularity. 9 Jun 2024 | vcfpy updated to version 0.13.8 | Python library for handling the variant call format. Differs from pyvcf in that it has the ability to modify per-sample genotype information. 9 Jun 2024 | htsbox updated to version r350 | HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files. While some of these tools are already part of the official SAMtools package, others are for niche use cases. 9 Jun 2024 | k8 updated to version 1.2 | javascript shell based on v8, but with fasta/fastq parser and the ability to open files on the filesystem 7 Jun 2024 | slivar updated to version 0.3.1 | slivar is a set of command-line tools that enables rapid querying and filtering of VCF files. It facilitates operations on trios and groups and allows arbitrary expressions using simple javascript. 6 Jun 2024 | rapids-singlecell updated to version 0.10.4 | Rapids-singlecell offers enhanced single-cell data analysis as a near drop-in replacement predominantly for scanpy.Utilizing GPU computing with cupy and Nvidia’s RAPIDS, it emphasizes high computational efficiency. 5 Jun 2024 | FFmpeg updated to version 7.0.1 | A complete, cross-platform solution to record, convert and stream audio and video. 4 Jun 2024 | stringtie updated to version 2.2.3 | 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. 4 Jun 2024 | novocraft updated to version 4.04.01 | Package includes aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties. 3 Jun 2024 | inkscape updated to version 1.3.2 | Inkscape is a Free and open source vector graphics editor 3 Jun 2024 | subread updated to version 2.0.6 | High-performance read alignment, quantification and mutation discovery 1 Jun 2024 | medaka updated to version 1.12.0 | 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. 31 May 2024 | verkko updated to version 2.1 | Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads. 31 May 2024 | ngsrelate updated to version 2.0 | NgsRelate can be used to infer relatedness, inbreeding coefficients and many other summary statistics for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes. 30 May 2024 | boost updated to version 1.85 | 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. 29 May 2024 | toga updated to version 1.1.7 | TOGA is a new method that integrates gene annotation, inferring orthologs and classifying genes as intact or lost. TOGA implements a novel machine learning based paradigm to infer orthologous genes between related species and to accurately distinguish orthologs from paralogs or processed pseudogenes. This tutorial explains how to get started using TOGA. It shows how to install and execute TOGA, and how to handle possible issues that may occur. |