| Updated | Application
| 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. 13 Sep 2024 | RepeatMasker updated to version 4.1.7-p1 | 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. 13 Sep 2024 | nvtop updated to version 3.1.0 | NVTOP stands for Neat Videocard TOP, a (h)top like task monitor for GPUs and accelerators. It can handle multiple GPUs and print information about them in a htop-familiar way. 13 Sep 2024 | gdc-client updated to version 2.3.0 | The GDC Data Transfer Tool provides an optimized method of transferring data to and from the GDC, and enables resumption of interrupted transfers. 12 Sep 2024 | abyss updated to version 2.3.9 | 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. 11 Sep 2024 | deeppolisher updated to version 0.1.0 | DeepPolisher is a transformer-based sequencing correction method similar to DeepConsensus. DeepPolisher is designed to identify errors in genome assemblies. DeepPolisher takes haplotype-specific reads aligned to phased assemblies and produces a VCF file containing potential errors in the assembly. 10 Sep 2024 | deepsomatic updated to version 1.6.1 | DeepSomatic is a google developed analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data. 8 Sep 2024 | MPSAN-MP updated to version 20240817 | The MPSAN_MP application employs neural networks implementing the Message Passing or Self-Attention mechanism for Molecular Property prediction. It takes as input a set of molecules represented by either graphs or SMILES strings. For each molecule, it predicts a propery value (PV), which may be either a discrete/binary label (classification task) or a continuous value (regression task). of molecular property prediction: This application is been be used as a biological example by the class #7 of the course "Deep Learning by Example on Biowulf". 5 Sep 2024 | verkko updated to version 2.2 | Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads. 5 Sep 2024 | SAMsrc updated to version v5-20210705 | Synthetic Aperture Magnetometry - The SANsrcV3 suite implements the latest advances in MEG source localization. 5 Sep 2024 | graphaligner updated to version 1.0.19 | Seed-and-extend program for aligning long error-prone reads to genome graphs. 4 Sep 2024 | quarto updated to version 1.5.57 | Quarto is an open-source scientific and technical publishing system built on Pandoc 4 Sep 2024 | homer updated to version 5.1 | HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. 3 Sep 2024 | Rosetta updated to version 2024.09 | The Rosetta++ software suite can perform de novo protein structure predictions, identify low free energy sequences for target protein backbones, predict the structure of a protein-protein complex from the individual structures of the monomer components, incorporate NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction, and more... 30 Aug 2024 | eog updated to version 42.0 | Eye of Gnome image viewer 29 Aug 2024 | Genome Browser updated to version 469 | 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. 29 Aug 2024 | boost updated to version 1.86 | 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. 28 Aug 2024 | postgresql updated to version 16.4 | PostgreSQL is a powerful, open source object-relational database system with over 35 years of active development that has earned it a strong reputation for reliability, feature robustness, and performance. 28 Aug 2024 | SciTE updated to version 5.5.2 | 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. 28 Aug 2024 | parallel updated to version 20240822 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 27 Aug 2024 | dorado updated to version 0.7.3 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 27 Aug 2024 | hyphy updated to version 2.5.62 | HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning. 27 Aug 2024 | Julia updated to version 1.10.4 | high level, dynamic language for technical computing 22 Aug 2024 | pangene updated to version 1.1 | Pangene constructs a pangenome gene graph in the GFA format from the miniprot alignment between a protein set and multiple genomes.. 22 Aug 2024 | miniprot updated to version 0.13 | Miniprot aligns protein sequences to whole genomes with splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. 22 Aug 2024 | uv updated to version 0.4.0 | An extremely fast Python package and project manager, written in Rust. 21 Aug 2024 | ANTs updated to version 2.5.3 | Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging. Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. 21 Aug 2024 | cmake updated to version 3.30.2 | CMake is a family of tools designed to build, test and package software. 20 Aug 2024 | chopper updated to version 0.9.0 | Filtering and trimming for long-read sequencing data (PacBio/ONT). 19 Aug 2024 | gfatools updated to version 0.5-r292-20240220 | gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA/BED. 19 Aug 2024 | connectome-workbench updated to version 2.0.0 | 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. 16 Aug 2024 | modkit updated to version 0.3.2 | 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. 15 Aug 2024 | fmriprep updated to version 24.0.1 | A Robust Preprocessing Pipeline for fMRI Data 15 Aug 2024 | mustache updated to version 1.3.3 | Mustache is a tool for identifying chromatin loops from HiC and MicroC contact maps 15 Aug 2024 | neoloopfinder updated to version ff83bcc | tool for identifying tumorigenic mechanisms and providing diagnostic and therapeutic targets. 14 Aug 2024 | cellpose updated to version 3.0.10 | A generalist algorithm for cellular segmentation with human-in-the-loop capabilities. 14 Aug 2024 | rliger updated to version 2.0.1 | R package: rliger. Linked Inference of Genomic Experimental Relationships. Use with rliger-R, rliger-Rscript. 14 Aug 2024 | mixcr updated to version 4.7.0 | MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data. 13 Aug 2024 | diann updated to version 1.9.1 | DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing 13 Aug 2024 | fragpipe updated to version 22.0 | FragPipe is a Java Graphical User Interface (GUI) and CLI workflow tool for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger. 13 Aug 2024 | diatracer updated to version 1.1.5 | diaTracer is a computational tool that enables spectrum-centric analysis of Bruker's diaPASEF data-independent acquisition proteomics data, facilitating direct (“spectral-library free”) peptide identification and quantification. Usually used via Fragpipe. 13 Aug 2024 | ionquant updated to version 1.10.27 | IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as part of FragPipe (recommended option), but can also be run as a command-line tool. 13 Aug 2024 | msfragger updated to version 4.1 | An ultrafast database search tool for peptide identification in mass spectrometry-based proteomics. 13 Aug 2024 | libfreetype updated to version 2.13.3 | FreeType is a freely available software library to render fonts. 12 Aug 2024 | spielbash updated to version 0.1.4 | Spielbash helps you automate asciicasts with asciinema. 12 Aug 2024 | eaglec updated to version 0.1.9 | Deep-Learning framework for predicting structural variations from bulk and single-cell contact maps. 12 Aug 2024 | openmm updated to version 8.1.2 | A high-performance toolkit for molecular simulation. Use it as an application, a library, or a flexible programming environment. It includes extensive language bindings for Python, C, C++, and even Fortran. 12 Aug 2024 | Chimera updated to version 1.18.0 | Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. 9 Aug 2024 | shasta updated to version 0.12.0 | De novo assembly from Oxford Nanopore reads 9 Aug 2024 | cgpbigwig updated to version 1.7.0 | BigWig manpulation tools using libBigWig and htslib 8 Aug 2024 | trgt updated to version 1.1.1 | 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. 8 Aug 2024 | nasm updated to version 2.16.03 | asssembler/disassembler for the intel x86 architecture 7 Aug 2024 | fzf updated to version 0.54.3 | 🌸 A command-line fuzzy finder 7 Aug 2024 | AnnotSV updated to version 3.4.2 | AnnotSV is a program designed for annotating Structural Variations (SV). This tool compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to i) interpret SV potential pathogenicity and ii) filter out SV potential false positives. 7 Aug 2024 | whatshap updated to version 2.3 | WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. 7 Aug 2024 | simvascular updated to version may-2023 | Cardiovascular Modeling and Simulation 6 Aug 2024 | Beagle updated to version 5.4_27May24 | 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 Aug 2024 | GT-Pro updated to version 1.0.1-20230507 | GT-Pro utilizes an exact matching algorithm to perform ultra-rapid and accurate genotyping of known SNPs from metagenomes. 2 Aug 2024 | idep updated to version 2.01 | iDEP (integrated Differential Expression and Pathway analysis) is shiny application for analyzing RNA-seq data 1 Aug 2024 | membrain-seg updated to version 0.0.5 | 3D membrane segmentation for cryo-electron tomography. 31 Jul 2024 | esm updated to version 3.0.1 | Code and pre-trained weights for Transformer protein language models from the Meta Fundamental AI Research Protein Team (FAIR) 30 Jul 2024 | paleomix updated to version 1.3.7 | the PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data 30 Jul 2024 | ImageMagick updated to version 7.1.1 | ImageMagick is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats. The ImageMagick tools are available by default (e.g. type 'convert') or use 'module load ImageMagick' to load the latest versions. 30 Jul 2024 | neovim updated to version 0.10.1 | Neovim is a refactor, and sometimes redactor, in the tradition of Vim (which itself derives from Stevie). It is not a rewrite but a continuation and extension of Vim. 29 Jul 2024 | HiFi-human-WGS updated to version 1.1.1 | Pacific Biosciences workflow for analyzing human PacBio whole genome sequencing data. 29 Jul 2024 | GATK updated to version 4.6.0.0 | GATK, from the Broad Institute, is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. 29 Jul 2024 | GenomeSyn updated to version 20240716 | GenomeSyn, implemented in Perl, is a bioinformatics tool for visualizing genome synteny and structural variations. It provides genome synteny visualization for two or three genomic sequences. Additionally, genome annotation can be uploaded to visualize various SVs among different genomes. 29 Jul 2024 | objtools updated to version 0.8.4 | Scripts for interacting with the Black Pearl/Vail tape object storage system. 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 | CCP4 updated to version 9.0.001 | CCP4 is a suite of programs for protein crystallography and structural biology. 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 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 |