August 2023 Newsletter
Our August newsletter includes twenty three new and updated titles for Mac and Linux. New software titles 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 660 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:
macOS: Installation Manager 2.6.17
Linux: Installation Manager 2.6.17
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
deepTools - a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data.
Updated versions:3.5.3 | OS X INTEL 3.5.3 | Linux 64
Snakemake - workflow management system is a tool to create reproducible and scalable data analyses.
Updated versions:7.32.3 | Linux 64 7.32.3 | OS X INTEL
DIAMOND - high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.
Updated versions:2.1.8 | Linux 64 2.1.8 | OS X INTEL
corset - software for clustering de novo assembled transcripts and counting overlapping reads.
Updated versions:1.09 | OS X INTEL 1.09 | Linux 64
R-pkgs-Biogrids - contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions:r4.2.3-20230807 | Linux 64
R - a free software environment for statistical computing and graphics.
Updated versions:4.2.3 | OS X INTEL 4.2.3 | Linux 64
spaceranger - Visium Spatial Software Suite for analyzing and visualizing spatial gene and protein expression data.
Updated versions:2.1.0 | Linux 64
EMA - Fast & accurate alignment of barcoded short-reads
Updated versions:0.6.2 | OS X INTEL 0.6.2 | Linux 64
lastz - a program for aligning DNA sequences, a pairwise aligner.
Updated versions:1.04.22 | Linux 64 1.04.22 | OS X INTEL
vcf2parquet - convert a vcf in parquet.
Updated versions:0.4.1 | Linux 64 0.4.1 | OS X INTEL
isoseq3 - Scalable De Novo Isoform Discovery
Updated versions:4.0.0 | Linux 64
PFP - tool to build the parse and the dictionary for VCF files using the approach described in Prefix-Free Parsing for Building Big BWTs.
Updated versions:0.3.9 | OS X INTEL 0.3.9 | Linux 64
KMCP - accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping.
Updated versions:0.9.3 | Linux 64 0.9.3 | OS X INTEL
abismal - a fast and memory-efficient mapper for short bisulfite sequencing reads.
Updated versions:3.2.0 | OS X INTEL 3.2.0 | Linux 64
msamtools - microbiome-related extension to samtools.
Updated versions:1.1.3 | Linux 64 1.1.3 | OS X INTEL
LevioSAM2 - Fast and accurate coordinate conversion between assemblies.
Updated versions:0.4.1 | OS X INTEL 0.4.1 | Linux 64
GATK - (Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.
Updated versions:4.4.0.0 | Linux 64 4.4.0.0 | OS X INTEL
STAR - (Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.
Updated versions:2.7.10b | Linux 64 2.7.10b | OS X INTEL
sdm - simple demultiplex tool for FASTQ demultiplexing and dereplication.
Updated versions:2.10 | Linux 64 2.10 | OS X INTEL
platon - plasmid contig classification and characterization for short read draft assemblies.
Updated versions:1.7 | Linux 64 1.7 | OS X INTEL
InSilicoSeq - sequencing simulator.
Updated versions:1.6.0 | Linux 64 1.6.0 | OS X INTEL
dnmtools - a set of tools for analyzing DNA methylation data from bisulfite sequencing
Updated versions:1.3.0 | OS X INTEL 1.3.0 | Linux 64
AGAT - (Another Gff Analysis Toolkit) a suite of tools to handle gene annotations in any GTF/GFF format.
Updated versions:1.2.0 | Linux 64 1.2.0 | OS X INTEL
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.
|
|
|
|
|
