||28 Mar 2023 ||afsample updated to version 2.2.0-38-g9f76c2a|
Protein folding, but more of it
|28 Mar 2023 ||hicmaptools updated to version 20230303|
hicmaptools is a command line tool to access HiC maps. The complete program provides multi-query modes and analysis tools.
|27 Mar 2023 ||bionetgen updated to version 0.7.9|
BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. BioNetGen is presently a mixture of Perl, C++, and Python.
|27 Mar 2023 ||AnnotSV updated to version 3.3.1|
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.
|27 Mar 2023 ||straw updated to version 1.3.1|
Straw is library which allows rapid streaming of contact data from .hic files.
|26 Mar 2023 ||smrtanalysis updated to version 220.127.116.11059|
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.
|23 Mar 2023 ||parallel updated to version 20230322|
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
|21 Mar 2023 ||Comsol updated to version 18.104.22.1686|
The COMSOL Multiphysics engineering simulation software environment facilitates all steps in the modeling process − defining your geometry, meshing, specifying your physics, solving, and then visualizing your results.
|21 Mar 2023 ||MySQL updated to version 8.0.32|
MySQL is an open-source relational database management system.
|21 Mar 2023 ||conda-prefix-replacement updated to version 0.1.1|
CPR resuscitates packages in new locations. It's a library for detecting files that have the absolute path of the build-time install prefix baked into them, and also for replacing those baked-in prefixes with new values when files are moved.
|21 Mar 2023 ||RELION updated to version 4.0.1|
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
|17 Mar 2023 ||bcl-convert updated to version 4.0.3|
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.
|16 Mar 2023 ||pyem updated to version 230315|
UCSF pyem is a collection of Python modules and command-line utilities for electron microscopy of biological samples.
|15 Mar 2023 ||multiqc updated to version 1.14|
aggregates results for various frequently used bioinformatics tools across multiple samples into a nice visual report
|14 Mar 2023 ||gunc updated to version 1.0.5|
Genome UNClutterer (GUNC) is a tool for detection of chimerism and contamination in prokaryotic genomes resulting from mis-binning of genomic contigs from unrelated lineages
|14 Mar 2023 ||pairtools updated to version 0.3.0; 1.0.2|
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.
|13 Mar 2023 ||pymc updated to version 5|
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.
|9 Mar 2023 ||napari updated to version 0.4.17|
napari is an image viewer.Can be used to annotate images.
|9 Mar 2023 ||model-angelo updated to version 0.2.2|
ModelAngelo is an automatic atomic model building program for cryo-EM maps.
|9 Mar 2023 ||3DSlicer updated to version 5.2.2|
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.
|8 Mar 2023 ||automake updated to version 1.16.5|
Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards.
|8 Mar 2023 ||m4 updated to version 1.4.19|
GNU M4 is an implementation of the traditional Unix macro processor.
|8 Mar 2023 ||autoconf updated to version 2.71|
Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages.
|6 Mar 2023 ||KmerGO2 updated to version 2.0.1|
KmerGO is a user-friendly tool to identify the group-specific sequences on two groups of high throughput sequencing datasets.
|3 Mar 2023 ||STAR updated to version 2.7.10b|
Spliced Transcripts Alignment to a Reference
|1 Mar 2023 ||Genome Browser updated to version 444|
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.
|28 Feb 2023 ||salmon updated to version 1.10.0|
a tool for quantifying the expression of transcripts using RNA-seq data.
|27 Feb 2023 ||postgresql updated to version 15.2|
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.
|27 Feb 2023 ||interproscan updated to version 5.60-92.0|
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.
|27 Feb 2023 ||EMAN2 updated to version 2.99|
EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.
|27 Feb 2023 ||seq2hla updated to version 2.3|
seq2HLA computationally determines human leukocyte antigen (HLA) genotypes of a sample using RNA-Seq sequencing reads.
|23 Feb 2023 ||intogen updated to version 2023.1|
Identifies cancer genes and pinpoints their putative mechanism of action across tumor types
|22 Feb 2023 ||samtools updated to version 1.17|
The samtools package now provides samtools, bcftools, tabix, and the underlying htslib library.
|22 Feb 2023 ||golang updated to version 1.20.1|
The Go programming language
|22 Feb 2023 ||xTea updated to version 0.1.9; 1.0.0|
xTea (x-Transposable element analyzer), is a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for shortread data, xTea can be applied to both short-read and long-read data. xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery.
|21 Feb 2023 ||Huygens updated to version 22.10.0-p4|
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.
|20 Feb 2023 ||stow updated to version 2.3.1|
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.
|19 Feb 2023 ||rmblast updated to version 2.13.0|
RMBlast is a RepeatMasker-compatible version of the standard NCBI blastn program. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program.
|17 Feb 2023 ||AutodockCrankprep updated to version 1.0|
"AutoDock CrankPep or ADCP is an AutoDock docking engine specialized for docking peptides. It combines technology form the protein folding filed with an efficient representation of a rigid receptor as affinity grids to fold the peptide in the context of the energy landscape created by the receptor."
|16 Feb 2023 ||apptainer updated to version 1.1.6|
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.
|16 Feb 2023 ||rclone updated to version 1.61.1|
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.
|15 Feb 2023 ||VEP updated to version 109|
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.
|14 Feb 2023 ||Mathematica updated to version 13.2.1|
Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language.
|13 Feb 2023 ||rvtests updated to version 2.1.0|
Rare Variant tests is a flexible software package for genetic association studies. It is designed to support unrelated individual or related (family-based) individuals
|13 Feb 2023 ||merfin updated to version 1.1|
Improved variant filtering and polishing via k-mer validation
|13 Feb 2023 ||CytoSig updated to version 0.1|
CytoSig is a data-driven infrastructure hosted by the National Cancer Institute. CytoSig includes both a database of target genes modulated by cytokines and a predictive model of cytokine signaling activity and regulatory cascade from transcriptomic profiles.
|13 Feb 2023 ||guppy updated to version 6.4.6|
Local accelerated basecalling for Nanopore data
|10 Feb 2023 ||topaz updated to version 0.2.5-ba91e19|
topaz is a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph and tomogram denoising using deep denoising models.
|10 Feb 2023 ||parmed updated to version 4.0.0|
Cross-program parameter and topology file editor and molecular mechanical simulator engine.
|10 Feb 2023 ||alphafold2 updated to version 2.3.1|
This package provides an implementation of the protein structure inference pipeline of AlphaFold v2.0.
|9 Feb 2023 ||philosopher updated to version 4.2.2;4.8.1|
Philosopher is fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. Philosopher is dependency-free and can analyze both traditional database searches and open searches for post-translational modification (PTM) discovery.
|8 Feb 2023 ||cellranger updated to version 7.1.0|
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.
|7 Feb 2023 ||trinity updated to version 2.15.1|
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.
|7 Feb 2023 ||genometools updated to version 1.6.2|
collection of bioinformatic tools
|6 Feb 2023 ||swarm updated to version 23.2.1|
Swarm is a script designed to simplify submitting a group of commands to the Biowulf cluster.
|3 Feb 2023 ||rosettafoldna updated to version 0.1|
Accurate prediction of nucleic acid and protein-nucleic acid complexes using RoseTTAFoldNA
|2 Feb 2023 ||arriba updated to version 2.3.0|
Arriba identifies gene fusions in RNA-Seq data. It also can detect other structural variants in genomic data, such as intron duplications and gene truncations.
|1 Feb 2023 ||oncodriveFML updated to version 2.2.0|
OncodriveFML is a method designed to analyze the pattern of somatic mutations across tumors in both coding and non-coding genomic regions to identify signals of positive selection, and therefore, their involvement in tumorigenesis.
|1 Feb 2023 ||oncodriveCLUSTL updated to version 1.1.1|
OncodriveCLUSTL is a sequence-based clustering algorithm to detect significant clustering signals across genomic regions. It is based based on a local background model derived from the simulation of mutations accounting for the composition of trior penta-nucleotide context substitutions observed in the cohort under study.
|1 Feb 2023 ||boost updated to version 1.81|
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.
|1 Feb 2023 ||biobakery_workflows updated to version 3.1|
bioBakery is a meta’omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of preconfigured analysis modules also joined into workflows for reproducibility. Each individual module has been developed to perform a particular task, e.g. quantitative taxonomic profiling or statistical analysis.
|31 Jan 2023 ||gitflow updated to version 0.4.2|
A collection of Git extensions to provide high-level repository operations for Vincent Driessen's branching model.
|31 Jan 2023 ||spaceranger updated to version 2.0.1|
10x pipeline for processing Visium spatial RNA-seq data
|30 Jan 2023 ||pbsuite updated to version 15.8.24|
The PBSuite contains two projects created for analysis of Pacific Biosciences long-read sequencing data: PBHoney and PBJelly. PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants. PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes.
|27 Jan 2023 ||velvet updated to version 1.2.10|
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454
|27 Jan 2023 ||distiller-nf updated to version 0.3.3|
A modular Hi-C mapping pipeline for reproducible data analysis, it was used for Micro-C analysis too.
|27 Jan 2023 ||sb_cli updated to version 0.25.0|
Use the Seven Bridges Command Line Interface (SB CLI) to programmatically access and automate your interaction with the Platform via the API. The CLI is called by a simple command: sb.
|25 Jan 2023 ||Acemd updated to version 3.5.1|
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.
|25 Jan 2023 ||bowtie2 updated to version 2.5.1|
A version of bowtie that's particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes
|24 Jan 2023 ||elastix updated to version 4.9; 5.1.0|
a toolbox for rigid and nonrigid registration of images.
|20 Jan 2023 ||focus updated to version 0.802|
FOCUS (Fine-mapping Of CaUsal gene Sets) is software to fine-map transcriptome-wide association study statistics at genomic risk regions. The software takes as input summary GWAS data along with eQTL weights and outputs a credible set of genes to explain observed genomic risk.
|20 Jan 2023 ||patchelf updated to version 0.17|
patchelf is a small utility to modify the dynamic linker and RPATH of ELF executables.
|19 Jan 2023 ||tensorflow updated to version 2.11.0|
TensorFlow is an end-to-end open source platform for machine learning. It has a comprehensive, flexible ecosystem of tools, libraries, and community resources that lets researchers push the state-of-the-art in ML and developers easily build and deploy ML-powered applications.
|18 Jan 2023 ||FEBio updated to version v4.0|
FEBio software suite implement a nonlinear implicit finite element (FE) framework, designed specifically for analysis in computational solid biomechanics. FEBio offers modeling scenarios, constitutive models, and boundary conditions, which are relevant to numerous applications in biomechanics. The open-source FEBio software is written in C++, with particular attention to scalar and parallel performance on modern computer architectures.
|18 Jan 2023 ||singularity updated to version 3.10.5|
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.
|17 Jan 2023 ||cmtk updated to version 3.3.2|
CMTK is a Software toolkit for computational morphometry of biomedical images. CMTK provides a set of command line tools for processing and I/O.
|13 Jan 2023 ||QuPath updated to version 0.4.1|
QuPath is open source software for bioimage analysis. It is often used for digital pathology applications because it offers a powerful set of tools for working with whole slide images - but it can be applied to lots of other kinds of image as well.
|12 Jan 2023 ||selscan updated to version 1.3.0; 2.0.0|
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.
|10 Jan 2023 ||GimmeMotifs updated to version 0.17.2|
GimmeMotifs is a pipeline for transcription factor motif analysis written in Python. It incorporates an ensemble of computational tools to predict motifs de novo from ChIP-sequencing data. Similar redundant motifs are compared using the weighted information content similarity score and clustered using an iterative procedure. A comprehensive output report is generated with several different evaluation metrics to compare and evaluate the results.
|6 Jan 2023 ||deeploc updated to version 2.0|
DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins. It is is able to predict one or more localizations for any given protein.
|6 Jan 2023 ||globus-timer-cli updated to version 0.2.9|
Command-line client for setting up and monitoring recurring or scheduled Globus transfers
|5 Jan 2023 ||MoChA updated to version 1.10.2; 1.11; 1.16|
MoChA is a bcftools extension to call mosaic chromosomal alterations starting from phased VCF files with either B Allele Frequency (BAF) and Log R Ratio (LRR) or allelic depth (AD)
|5 Jan 2023 ||Freesurfer updated to version 7.3.2|
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.
||28 Mar 2023||NCBI nr||Fasta||/fdb/fastadb/nr.fas||28 Mar 2023||SwissProt||Fasta||/fdb/fastadb/swissprot.aa.fas||28 Mar 2023||Protein Data Bank||Fasta||/fdb/fastadb/pdb.aa.fas||28 Mar 2023||NCBI Taxonomy||taxonomy||/fdb/taxonomy||25 Mar 2023||NCBI nt||Blast||/fdb/blastdb/nt||25 Mar 2023||NCBI nr||Blast||/fdb/blastdb/nr||25 Mar 2023||SwissProt||Blast||/fdb/blastdb/swissprot||25 Mar 2023||Protein Data Bank||Blast||/fdb/blastdb/pdbaa||21 Mar 2023||NCBI nt||Fasta||/fdb/fastadb/nt.fas||13 Mar 2023||Protein Data Bank||Blast||/fdb/blastdb/pdbnt||03 Feb 2023||Human Genome hg19||Fasta||/fdb/genome/human-feb2009/||02 Feb 2023||Cambridge Structural Database||CSD||/usr/local/apps/CSD||30 Jan 2023||ANNOVAR||ANNOVAR||/fdb/annovar/current||08 Jan 2023||Mouse Genome (Mus musculus) mm8||MySQL||NIH mirror of UCSC Genome Browser|