| Updated | Application
| 19 Nov 2024 | isoquant updated to version 3.6.2 | IsoQuant is used to analyze long read RNA sequencing data 18 Nov 2024 | cellranger updated to version 9.0.0 | Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. 18 Nov 2024 | libjpeg-turbo updated to version 3.0.90 | libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, NEON) to accelerate baseline JPEG compression and decompression on x86, x86-64, and ARM systems. 18 Nov 2024 | PMT (pb-metagenomics-tools) updated to version 2.1.0. | PB-metagenomics-tools is a suite of tools for performing metagenomic analyses using HiFi sequencing data. It comprises four pipelines: HiFi-MAG-Pipeline, Taxonomic-Profiling-Diamond-Megan, Taxonomic-Profiling-Minimap-Megan and Taxonomic-Profiling-Sourmash. 18 Nov 2024 | steinbock updated to version 0.16.3 | steinbock is a toolkit for processing multiplexed tissue images 16 Nov 2024 | rgt updated to version 1.0.2 | Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data. http://www.regulatory-genomics.org 15 Nov 2024 | diann updated to version 1.9.2 | DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing 15 Nov 2024 | pychopper updated to version 2.7.10 | Pychopper v2 is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads. 14 Nov 2024 | fastp updated to version 0.24.0 | A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. 13 Nov 2024 | sniffles updated to version 2.5.2 | 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. 13 Nov 2024 | quast updated to version 5.3.0 | 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. 13 Nov 2024 | Genome Browser updated to version 473 | 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. 8 Nov 2024 | NAMD updated to version 3.0.1 | NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. VMD, the associated molecular visualization program, is also available. 8 Nov 2024 | R updated to version 4.4.2 | 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, ...). 8 Nov 2024 | spiwalk updated to version 1.15.0 | Simulates the behavior of spins under a specific # MR sequence within a microvascular network. 8 Nov 2024 | uv updated to version 0.5.0 | An extremely fast Python package and project manager, written in Rust. 7 Nov 2024 | PhaseFinder updated to version 1.0-20240110 | PhaseFinder detects DNA inversion mediated phase variation in bacterial genomes using genomic or metagenomic sequencing data. It works by identifying regions flanked by inverted repeats, mimicking their inversion in silico, and identifying regions where sequencing reads support both orientations. 7 Nov 2024 | mriqc updated to version 24.0.2 | MRIQC is an MRI quality control tool 7 Nov 2024 | rseqc updated to version 5.0.4 | Rseqc comprehensively evaluate RNA-seq datasets generated from clinical tissues or other well annotated organisms such as mouse, fly and yeast. 6 Nov 2024 | braker updated to version 3.0.8 | A pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes. 6 Nov 2024 | Freesurfer updated to version 8.0.0-beta | 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. 6 Nov 2024 | connectome-workbench updated to version 2.0.1 | Tools to browse, download, explore, and analyze data from the Human Connectome Project (HCP). Allows users to compare their own data to that of the HCP. 5 Nov 2024 | uropa updated to version 4.0.3 | UROPA is a command line based tool for genomic region annotation 5 Nov 2024 | Beagle updated to version 5.4_29Oct24 | Beagle is a package for imputing genotypes, inferring haplotype phase, and performing genetic association analysis. BEAGLE is designed to analyze large-scale data sets with hundreds of thousands of markers genotyped on thousands of samples. 5 Nov 2024 | tedana updated to version 24.0.2 | Tedana is an application to denoise multi-echo fMRI datasets 5 Nov 2024 | fmriprep updated to version 24.1.1 | A Robust Preprocessing Pipeline for fMRI Data 4 Nov 2024 | pigz updated to version 2.8 | pigz (parallel implementation of gzip) is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. 4 Nov 2024 | nodejs updated to version 22.11.0 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 4 Nov 2024 | LAST updated to version 1595 | LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially geared toward:
4 Nov 2024 | ant updated to version 1.10.15 | Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. 4 Nov 2024 | Mathematica updated to version 14.1.0 | Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language. 4 Nov 2024 | PartekFlow updated to version 12.2.0 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 3 Nov 2024 | Mascot updated to version 3.0 | The Mascot search engine uses mass spectrometry data to identify proteins from primary sequence databases. Mascot searches can be run directly on the NIH Mascot server at https://biospec.nih.gov, or by using the Mascot daemon on your own desktop PC. 1 Nov 2024 | dorado updated to version 0.8.2 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 31 Oct 2024 | medaka updated to version 2.0.1 | 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. 31 Oct 2024 | trinity updated to version 2.15.2 | 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. 31 Oct 2024 | jvarkit updated to version 20240825 | Java tools for bioinformatics 30 Oct 2024 | biomodal updated to version 1.1.0 | biomodal duet multiomics solution bioinformatics pipeline 29 Oct 2024 | svfsi updated to version 7bdb74c | Finite element solver for computational modeling of the cardio vascular system. 28 Oct 2024 | DEPICT updated to version v1_rel194 | DEPICT is an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. DEPICT is not limited to genes with established functions and prioritizes relevant gene sets for many phenotypes. 28 Oct 2024 | VADR updated to version 1.6.4 | 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. 28 Oct 2024 | LoMA updated to version 1.1.3. | LoMA is localized assembly method that constructs highly accurate consensus sequences (CSs) from long reads. LoMA's algorithm employs minimap2 and MAFFT and classifies diploid haplotypes based on structural variants and CSs. It allows analyzing human samples sequenced with the Oxford Nanopore sequencer. 24 Oct 2024 | novocraft updated to version 4.04.02 | 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. 24 Oct 2024 | bpipe updated to version 0.9.13 | Bpipe provides a platform for running big bioinformatics jobs 23 Oct 2024 | mc updated to version 4.8.32 | GNU Midnight Commander is a visual file manager, with a feature rich full-screen text mode application that allows you to copy, move and delete files and whole directory trees, search for files and run commands in the subshell. Type module load mc and then the command mc to get started. 23 Oct 2024 | texinfo updated to version 7.1.1 | Texinfo is the official documentation format of the GNU project 23 Oct 2024 | SciTE updated to version 5.5.3 | 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 Oct 2024 | parallel updated to version 20241022 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 22 Oct 2024 | fastq_screen updated to version 0.16.0 | 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. 22 Oct 2024 | diamond updated to version 2.1.9 | 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. 21 Oct 2024 | singularity updated to version 4.1.5 | 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. 18 Oct 2024 | msisensor-pro updated to version 1.3.0 | evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. 18 Oct 2024 | picard updated to version 3.3.0 | 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. 17 Oct 2024 | pggb updated to version 0.7.0 | pangenome graph builder. 17 Oct 2024 | hifiasm updated to version 0.20.0 | Hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads. Its latest release supports telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore reads. It can produce better haplotype-resolved assemblies when given parental short reads or Hi-C data. 15 Oct 2024 | rust updated to version 1.81.0 | A language empowering everyone to build reliable and efficient software. 15 Oct 2024 | Aspera updated to version 4.2.12 | High-speed fasp-powered file transfers. Mostly used to download data from NCBI, which has an Aspera server. See the data transfer page for details. 15 Oct 2024 | scvitools updated to version 1.2.0 | scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data primarily developed and maintained by the Yosef Lab at UC Berkeley. 10 Oct 2024 | FSL updated to version 6.0.7.14 | FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data. 8 Oct 2024 | svsolver updated to version cf1e3b3 | Parallel computational fluid dynamics (CFD) finite element solver incorporating boundary conditions useful for blood flow simulations 7 Oct 2024 | golang updated to version 1.23.2 | The Go programming language 7 Oct 2024 | globus-cli updated to version 3.30.1 | Globus command line interface 5 Oct 2024 | snakemake updated to version 8.16.0 | 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. 4 Oct 2024 | selscan updated to version 2.0.3 | selscan is a tool for haplotype-based scans to detect natural selection, which are useful to identify recent or ongoing positive selection in genomes. It is an efficient multithreaded application that implements Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and Cross-population EHH (XPEHH). selscan accepts phased genotypes in multiple formats, including TPED. 4 Oct 2024 | scFEA updated to version 1.1 | A graph neural network model to estimate cell-wise metabolic using single cell RNA-seq data 3 Oct 2024 | pairtools updated to version 1.1.0 | Pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment. Pairtools perform various operations on Hi-C pairs and occupy the middle position in a typical Hi-C data processing pipeline. Pairtools aim to be an all-in-one tool for processing Hi-C pairs. 2 Oct 2024 | iphop updated to version 1.3.3 | iPHoP stands for Integrated Phage Host Prediction. It is an automated command-line pipeline designed to predict the host genus of novel bacteriophages and archaeoviruses based on their genome sequences. 2 Oct 2024 | deepdewedge updated to version 240913 | DeepDeWedge is A Deep Learning Method for Simultaneous Denoising and Missing Wedge Reconstruction in Cryogenic Electron Tomography". 1 Oct 2024 | bcl-convert updated to version 4.1.23 | The Illumina BCL Convert is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. BCL Convert also provides adapter handling (through masking and trimming) and UMI trimming and produces metric outputs. 30 Sep 2024 | spaceranger updated to version 3.1.1 | 10x pipeline for processing Visium spatial RNA-seq data 30 Sep 2024 | Phenix updated to version 1.21.2-5419 | PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods. 26 Sep 2024 | mise updated to version 2024.9.9 | mise is a development environment setup tool. Using its .mise.toml config file, you'll have a consistent way to setup and interact with your projects no matter what language they're written in. 25 Sep 2024 | flye updated to version 2.9.5 | Fast and accurate de novo assembler for single molecule sequencing reads 24 Sep 2024 | samtools updated to version 1.21 | The samtools package now provides samtools, bcftools, tabix, and the underlying htslib library. 24 Sep 2024 | RBNS_pipeline updated to version 20240907 | The BNS (RNA Bind-N-Seq Analysis) pipeline is a set of bioinformatics tools to analyze data from high-throughput sequencing experiments of protein-bound RNAs. The current version includes read splitting, calculation of kmer frequencies and enrichments, QC metrics, production of motif sequence logos, and RNA secondary structure analysis. 23 Sep 2024 | trgt updated to version 1.2.0 | 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 can also create a visualization of reads overlapping the repeats. 23 Sep 2024 | stow updated to version 2.4.1 | 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. 23 Sep 2024 | kallisto updated to version 0.51.1 | 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. 23 Sep 2024 | modkit updated to version 0.4.1 | 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. 23 Sep 2024 | eza updated to version 0.19.4 | A modern, maintained replacement for ls. A replacement for the now-unmaintained exa. 19 Sep 2024 | Hyperqueue updated to version 0.19.0 | HyperQueue (HQ) lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups tasks into SLURM/PBS jobs and distributes them to fully utilize allocated nodes. 19 Sep 2024 | pod5 updated to version 0.3.15 | Tool for manipulating the pod5 format of nanopore reads 17 Sep 2024 | MotionCor2 updated to version 1.6.4 | 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. |