May 2025 Newsletter
Our May software update includes nineteen new and updated titles. Our new R package search tool lets you easily find packages of interest and shows which versions of BioGrids R already contain that package.
New software titles and R packages can be requested by sending email to help@biogrids.org or filling out our Software Request Form.
Remote Working Help
The BioGrids Wiki provides step by step instructions for installing BioGrids software on a local laptop or desktop machine. If you prefer a live demonstration, or run into trouble, please contact help@biogrids.org. We can set up a Zoom meeting to assist you.
Cite BioGrids
If your use of BioGrids supplied software was an important element in your publication, please include the following statement in your work:
"Software used in the project was installed and configured by BioGrids
(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)"
See our Grant Support page for additional details.
Register here to try out our software installer, which allows users to choose from over 770 bioinformatics and life sciences tools that can be installed as ready-to-run applications on Mac or Linux machines with the click of a button or a short command from the CLI. No need to worry about dependencies or compilation.
BioGrids is supported by a team of scientists and engineers at HMS. We provide direct support to BioGrids members. This includes all aspects of software installation and management. If you need assistance of any kind please send a note to: help@biogrids.org.
BioGrids Quickstart
The latest version of the BioGrids Installation Manager is available for Linux and MacOS computers from the BioGrids Wiki QuickStart page.
Start the BioGrids environment:
source /programs/biogrids.shrc
List available titles (Linux):
cat /programs/x86_64-linux/biogrids_x86_64-linux
List available titles (Mac):
cat /programs/i386-mac/biogrids_i386-mac
Get version and override info:
biogrids-info -l star
Get list of executables for a title:
biogrids-list star
Need more help? Send mail to: help@biogrids.org
Software Updates
kb-python - is a python package for processing single-cell RNA-sequencing. It wraps the kallisto | bustools single-cell RNA-seq command line tools in order to unify multiple processing workflows.
Updated versions:0.29.4 | Linux 64 0.29.4 | OS X INTEL
repaq - A tool to compress FASTQ files with ultra-high compression ratio and high speed. repaq supports compressing the FASTQ to .rfq or .rfq.xz formats. Compressing to .rfq is ultra fast, while compressing to .rfq.xz provides very high compression ratio.
Updated versions:0.5.0 | OS X INTEL 0.5.0 | Linux 64
dysgu - (pronounced duss-key) is a set of command line tools and python-API, for calling structural variants using paired-end or long read sequencing data.
Updated versions:1.8.4 | Linux 64 1.8.4 | OS X INTEL
bamtools - a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.
Updated versions:2.5.3 | Linux 64 2.5.3 | OS X INTEL
VCFtools - a program package designed to provide easily accessible methods for working with complex genetic variation data in the form of VCF files, such as those generated by the 1000 Genomes Project.
Updated versions:0.1.17 | Linux 64
antiSMASH - (antibiotics and Secondary Metabolite Analysis SHell) allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
Updated versions:8.0.0 | Linux 64 8.0.0 | OS X INTEL
Cell Ranger - a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Updated versions:8.0.1 | Linux 64 7.1.0 | Linux 64 6.1.2 | Linux 64 6.0.1 | Linux 64 4.0.0 | Linux 64 2.1.1 | Linux 64
BISCUIT - a utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data. It was written to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data.
Updated versions:1.7.0.20250512 | OS X INTEL 1.7.0.20250512 | Linux 64
SVDSS - a method for structural variations discovery from accurate long reads (e.g PacBio HiFi), based on the notion of sample-specific strings (SFS, or simply specific strings).
Updated versions:2.1.0 | Linux 64
BioPhi - an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.
Updated versions:1.0.11 | Linux 64 1.0.11 | OS X INTEL
BWA - (Burrows-Wheeler Aligner) a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
Updated versions:0.7.19 | Linux 64 0.7.19 | OS X INTEL
pyPINTS - Explore distal transcriptional regulatory elements (TREs) identified from nascent-transcript sequencing.
Updated versions:1.2.0 | Linux 64 1.2.0 | OS X INTEL
nextclade - SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
Updated versions:3.13.2 | Linux 64
Flye - a fast and accurate de novo assembler for single molecule sequencing reads.
Updated versions:2.9.6 | Linux 64
CapCruncher - is designed to process Capture-C, Tri-C and Tiled-C data. Unlike other pipelines that are designed to process Hi-C or Capture-HiC data, the filtering steps in CapCruncher are specifically optimized for these datasets.
Updated versions:0.3.14 | OS X INTEL 0.3.14 | Linux 64
oarfish - is a program for quantifying transcript-level expression from long-read (i.e. Oxford nanopore cDNA and direct RNA and PacBio) sequencing technologies.
Updated versions:0.8.1 | OS X INTEL 0.8.1 | Linux 64
AlphaFold - an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.
Updated versions:3.0.1 | Linux 64 3.0.0 | Linux 64
R - a free software environment for statistical computing and graphics.
Updated versions:4.4.2 | OS X INTEL 4.2.3 | OS X INTEL 4.4.2 | Linux 64 4.2.3 | Linux 64
PyTorch - an open source deep learning platform that provides a seamless path from research prototyping to production deployment.
Updated versions:0.4.1 | OS X INTEL 1.6.0 | OS X INTEL 1.7.0 | OS X INTEL 1.8.1 | OS X INTEL 2.6.0 | OS X INTEL 2.6.0 | Linux 64
Software Training
Center for Computational Biomedicine
The Center for Computational Biomedicine (CCB) Fall newsletter contains training and collaboration opportunities.
HMS Research Computing
HMS Research Computing User Training
Bioinformatics Support
Need help getting software installed on new machines? Have you been planning to try Amazon Web Services (AWS) cloud computing?
BioGrids can help you get started. We have expertise in bioinformatics, programming, workflow development and high performance computing.
We improve the collection with feedback from the community.
Want to see a new application in BioGrids?
Let us know: help@biogrids.org
BioGrids is supported by Harvard Medical School and Boston Children's Hospital and relies on a framework that was developed by SBGrid.
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