| Updated | Application
| 26 Dec 2024 | gapstop updated to version 0.3 | GPU-Accelerated Python gapSTOP for Template Matching is an open-source SW for fast template matching (TM) in cryo electron tomograms that is based on TM routines from STOPGAP. 26 Dec 2024 | locscale updated to version 2.2.9a | LocScale is a reference-based local amplitude scaling tool using prior model information to improve contrast of cryo-EM density maps. It can be helpful in the common case of resolution variation in the 3D reconstruction and it can be used as an alternative to other commonly applied map sharpening methods. 26 Dec 2024 | Open OnDemand updated to version 3.1.10 | The Open OnDemand interface allows you to work on the Biowulf cluster via your web browser. You can utilize select interactive web applications like Jupyter, RStudio or VS Code directly without logging in via traditional SSH. You can also access graphical applications via a familiar interface running on compute nodes. 26 Dec 2024 | texinfo updated to version 7.2 | Texinfo is the official documentation format of the GNU project 26 Dec 2024 | gnuplot updated to version 6.0.2 | 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. 26 Dec 2024 | parallel updated to version 20241222 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 23 Dec 2024 | recovar updated to version 20241210 | RECOVAR is a software tool for analyzing different conformations in heterogeneous cryo-EM and cryo-ET datasets. RECOVAR can reconstruct high-resolution volumes, estimate conformational density and low free-energy motions, and automatically identify subsets of images with a particular volume feature. 23 Dec 2024 | lipidens updated to version 1.0.0 | LipIDens is a pipeline for simulation assisted interpretation of lipid or lipid-like densities in e.g. cryogenic electron microscopy (cryo-EM) structures of membrane proteins. The protocol can be used to establish CG simulations, analyse lipid binding sites using PyLipID, screen, rank and process PyLipID outputs and establish atomistic simulations to refine lipid binding poses. 20 Dec 2024 | interproscan updated to version 5.72-103.0 | InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium. 20 Dec 2024 | transcript_clean updated to version 2.1 | TranscriptClean is a Python program that corrects mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome. It is designed for use with sam files from the PacBio Iso-seq and Oxford Nanopore transcriptome sequencing technologies 19 Dec 2024 | SciTE updated to version 5.5.4 | 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. 19 Dec 2024 | ChimeraX updated to version 1.9 | UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. 19 Dec 2024 | saturn updated to version 6906abf | Saturn is a deep learning approach that couples gene expression with protein representations learnt using large protein language models for cross-species integration. The key idea in SATURN is to map cells from all datasets to a shared space of functionally related genes that we name macrogenes. Using macrogenes, SATURN is uniquely able to detect functionally related genes co-expressed across species. 18 Dec 2024 | IMOD updated to version 5.1.0 | 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. 18 Dec 2024 | QIIME updated to version 2024.10 | 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). 18 Dec 2024 | cutadapt updated to version 5.0 | 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. 18 Dec 2024 | aretomo3 updated to version 2.0.3 | AreTomo3 is a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection. Integrating MotionCor3, AreTomo2, and GCtfFind in a single application, AreTomo3 has established an autonomous preprocessing pipeline that, whenever a new tilt series is collected, can activate and repeat itself from correction of beam induced motion and assembling tilt series to CTF estimation and correction, tomographic alignment, and 3D reconstruction throughout entire session of data collection without human intervention. 17 Dec 2024 | LAST updated to version 1607 | LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially geared toward:
17 Dec 2024 | sniffles updated to version 2.5.3 | 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. 17 Dec 2024 | warp updated to version 2.0.0dev31 | Warp is a set of tools for cryo-EM and cryo-ET data processing including: Warp, M, WarpTools, MTools, MCore, and Noise2Map. 17 Dec 2024 | dorado updated to version 0.9.0 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 16 Dec 2024 | smrtanalysis updated to version 25.1 | SMRT® Analysis is a bioinformatics software suite available for analysis of DNA sequencing data from Pacific Biosciences’ SMRT technology. Users can choose from a variety of analysis protocols that utilize PacBio® and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences. 16 Dec 2024 | genotools updated to version 1.3.2 | GenoTools is a suite of automated genotype data processing steps written in Python. The core pipeline was built for Quality Control and Ancestry estimation of data in the Global Parkinson's Genetics Program (GP2). 16 Dec 2024 | AreTomo2 updated to version 1.1.2 | A multi-GPU accelerated software package that fully automates motion-corrected marker-free tomographic alignment and reconstruction. It is improved version of AreTomo that allow multi-gpu parallelization and better tilt-series alignment. 16 Dec 2024 | HLA-LA updated to version 1.0.4 | Fast HLA type inference from whole-genome data. Previously known as HLA-PRG-LA. 16 Dec 2024 | cellbender updated to version 0.3.2 | CellBender is a software package for eliminating technical artifacts from high-throughput single-cell omics data, including scRNA-seq, snRNA-seq, and CITE-seq. 15 Dec 2024 | PartekFlow updated to version 12.3.0 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 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 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. 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 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 | 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. |