| Updated | Application
| 13 Dec 2024 | blender updated to version 4.3 | Blender is the free and open source 3D creation suite. Blender on Biowulf is meant for command-line rendering. 12 Dec 2024 | BEAST updated to version 10.5.0,2.6.7 | BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences. 12 Dec 2024 | foldseek updated to version 9-427df8a | Fast structural similarity search 12 Dec 2024 | cdnacupcake updated to version 29.0.0 | Miscellaneous collection of Python and R scripts for processing Iso-Seq data 11 Dec 2024 | portal_client updated to version 1.4.5 | Portal_client is Python-based client for downloading data made available through portals powered by the GDC-based portal system. There are several portals running on the internet to support various research efforts. Notably, the Neuroscience Multi-omic Archive (NeMO, https://nemoarchive.org/) and the Human Microbiome Project Data Analysis and Coordination Center (hmpdacc.org) use the portal to enable data exploration and download. The client accepts a manifest file as an input. This file contains URLs to the files to be downloaded. Manifest files can be generated using the shopping cart functionality of the portal's query interface. 11 Dec 2024 | bakta updated to version 1.10.2 | Rapid & standardized annotation of bacterial genomes, MAGs & plasmids 10 Dec 2024 | hifiasm updated to version 0.23.0 | 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. 10 Dec 2024 | nodejs updated to version 22.12.0 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 10 Dec 2024 | ChimeraX updated to version 1.8 | UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. 9 Dec 2024 | dorado updated to version 0.8.3 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 9 Dec 2024 | deepvariant updated to version 1.8.0 | DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. 5 Dec 2024 | ccpem updated to version 1.7.0 | The Collaborative Computational Project for electron cryo-microscopy (CCP-EM) supports users and developers in biological cryogenic EM. 4 Dec 2024 | Qt updated to version 5.15.16 | Qt is a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms with little or no change in the underlying codebase, while still being a native application with native capabilities and speed. 4 Dec 2024 | xpdf updated to version 4.05 | 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. 4 Dec 2024 | alphafold3 updated to version 3.0.0 | This package provides an implementation of the inference pipeline of AlphaFold 3 4 Dec 2024 | virtualgl updated to version 3.1.1 | VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration. 2 Dec 2024 | Huygens updated to version 24.10 | 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. 2 Dec 2024 | model-angelo updated to version 1.0.13 | ModelAngelo is an automatic atomic model building program for cryo-EM maps. 2 Dec 2024 | Genome Browser updated to version 474 | 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. 2 Dec 2024 | automake updated to version 1.17.0 | Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. 30 Nov 2024 | biomodal updated to version 1.1.3 | biomodal duet multiomics solution bioinformatics pipeline 29 Nov 2024 | spaceranger updated to version 3.1.2 | 10x pipeline for processing Visium spatial RNA-seq data 27 Nov 2024 | novasta updated to version 1.1 | Installed with one user's request for their cryo-ET classification of the nuclear pore complex C++ version of subtomogram averaging (SA) scripts from TOM/AV3 package https://doi.org/10.1073/pnas.0409178102. Both CPU and GPU parallelization is supported although the latter performs significantly worse, build against CUDA10. Recommend the user to only cpus. 27 Nov 2024 | cryosieve updated to version 1.2.8 | CryoSieve is an advanced software solution designed for particle sorting/sieving in single particle analysis (SPA) for Cryogenic Electron Microscopy (cryo-EM). 27 Nov 2024 | cryocare updated to version 0.3.0 | Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data: utilizes advanced image processing algorithms to enhance the quality of images obtained from Cryo-TEM (Cryo-Transmission Electron Microscopy) by selectively improving the contrast and detail of the important features within the image while minimizing noise, effectively making the data more interpretable for analysis, particularly in structural biology applications. 27 Nov 2024 | surface_morphometrics updated to version 1.1 | Surface_morphometrics: A pipeline of tools to generate robust open mesh surfaces from voxel segmentations of biological membranes using the Screened Poisson algorithm, calculate morphological features including curvature and membrane-membrane distance using pycurv's vector voting framework, and tools to convert these orphological quantities into morphometric insights. 26 Nov 2024 | cryopros updated to version 1.0.0 | CryoPROS is a computational framework specifically designed to tackle misalignment errors caused by preferred orientation issues in single-particle cryo-EM. 26 Nov 2024 | alphapept updated to version 0.5.0 | AlphaPept: a modern and open framework for MS-based proteomics 26 Nov 2024 | trgt updated to version 1.4.1 | 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. 26 Nov 2024 | nnUNet updated to version 2.4.2 | nnU-Net is a PyTorch-based semantic segmentation application. It will analyze the provided training cases and automatically configure a matching U-Net-based segmentation pipeline. 26 Nov 2024 | EDTA updated to version 2.2.2 | The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 26 Nov 2024 | lammps updated to version 29Aug2024 | LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. It runs on a variety of different computer systems, including single processor systems, distributed-memory machines with MPI, and GPU and Xeon Phi systems. LAMMPS is open source software, released under the GNU General Public License. 25 Nov 2024 | straglr updated to version 1.5.3 | Tandem repeat expansion detection or genotyping from long-read alignments 23 Nov 2024 | parallel updated to version 20241122 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 22 Nov 2024 | CADD updated to version 1.7.2 | CADD (Combined Annotation Dependent Depletion) is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. Currently, it supports the builds: GRCh37/hg19 and GRCh38/hg38. 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. 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 | 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. 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 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 | 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. |