March 2023 Newsletter
Our March newsletter includes twenty eight new and updated titles for Mac and Linux. This includes R version 4.2.3 with over 750 packages available in r-pkgs-BIOGRIDS. New software titles can be requested by sending email to help@biogrids.org or filling out our Software Request Form.
HMS Research Computing 2023 Spring User Training courses are now open for registration. See the list of classes and registration link at the end of this newsletter.
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
R - a free software environment for statistical computing and graphics.
Versions: 4.2.3 | MacOS | Linux 64
PBSIM2 - a simulator for long read sequencers with a novel generative model of quality scores.
Versions: 2.0.1 | OS X INTEL 2.0.1 | Linux 64
Winnowmap - a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.
Versions: 2.03 | OS X INTEL 2.03 | Linux 64
VerifyBamID2 - a robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
Versions: 2.0.1 | OS X INTEL 2.0.1 | Linux 64
Flye - fast and accurate de novo assembler for single molecule sequencing reads.
Versions: 2.9.2 | Linux 64 2.9.2 | OS X INTEL
perbase - per-base metrics on BAM/CRAM files.
Versions: 0.8.5 | OS X INTEL 0.8.5 | Linux 64
LRez - standalone tool and library for working with barcoded linked-reads.
Versions: 2.2.4 | Linux 64 2.2.4 | OS X INTEL
fpa - Filter Pairwise Alignment filter long read mapping information to save disk space.
Versions: 0.5.1 | OS X INTEL 0.5.1 | Linux 64
Rustyread - long-read simulator.
Versions: 0.4.1 | Linux 64 0.4.1 | OS X INTEL
Genion - characterizing gene fusions using long transcriptomics reads.
Versions: 1.1.1 | Linux 64 1.1.1 | OS X INTEL
Assembled Genomes Compressor - (AGC) is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans).
Versions: 3.0 | OS X INTEL 3.0 | Linux 64
TGS-GapCloser - a gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.
Versions: 1.2.1 | Linux 64 1.2.1 | OS X INTEL
GraphAligner - sequence to graph aligner for long reads.
Versions: 1.0.17 | Linux 64 1.0.17 | OS X INTEL
Fiji - an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure.
Versions: 2.9.0 | Linux 64 2.9.0 | OS X INTEL
megadepth - an efficient tool for extracting coverage related information from RNA and DNA-seq BAM and BigWig files.
Versions: 1.2.0 | Linux 64 1.2.0 | OS X INTEL
ImageMagick - a software suite to create, edit, compose, or convert bitmap images.
Versions: 7.1.1-3 | OS X INTEL 7.1.1-3 | Linux 64
Hifiasm - haplotype-resolved assembler for accurate Hifi reads.
Versions: 0.19.3 | Linux 64 0.19.3 | OS X INTEL
Scallop-LR - reference-based transcriptome assembler for long-reads RNA-seq data.
Versions: 0.9.2 | Linux 64 0.9.2 | OS X INTEL
CITE-seq-Count - count antibody TAGS from a CITE-seq and/or cell hashing experiment.
Versions: 1.4.4 | Linux 64 1.4.4 | OS X INTEL
dsh-bio - tools for BED, FASTA, FASTQ, GAF, GFA1/2, GFF3, PAF, SAM, and VCF files.
Versions: 2.2 | Linux 64 2.2 | OS X INTEL
krakenuniq - metagenomics classifier with unique k-mer counting for more specific results.
Versions: 1.0.3 | Linux 64 1.0.3 | OS X INTEL
DIAMOND - a 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.
Versions: 2.1.4 | Linux 64 2.1.4 | OS X INTEL
MethylDackel - process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them.
Versions: 0.6.1 | Linux 64 0.6.1 | OS X INTEL
deepTools - a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
Versions: 3.5.1 | Linux 64 3.5.1 | OS X INTEL
FFmpeg - a complete, cross-platform solution to record, convert and stream audio and video.
Versions: 5.1.2 | Linux 64 5.1.2 | OS X INTEL
pbmm2 - a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments.
Versions: 1.7.0 | Linux 64 1.10.0 | Linux 64 1.7.0 | OS X INTEL
minorseq - PacBio Minor Variant Calling and Phasing Tools.
Versions: 1.12.0 | Linux 64
bam2fastx - provides conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data.
Versions: 1.3.1 | Linux 64 1.3.1 | OS X INTEL
IGV - (Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
Versions: 2.16.0 | Linux 64 2.16.0 | 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 2023 Spring User Training is now open.
| Class |
Date |
Time |
| Intro to O2 |
Apr. 12, 2023 |
10am to 12pm |
| Intro to O2 Portal |
May 3, 2023 |
10am to 11pm |
Where Should I Put My Data?
Understanding Data Storage at HMS |
May 10, 2023 |
10am to 11am |
| Intermediate O2 |
May 17, 2023 |
10am to 12pm |
| Intro to Python |
May 24, 2023 |
10am to 12pm |
RCBio: Easy and Quick HPC Pipeline
Builder and Runner |
May 31, 2023 |
10am to 11am |
| Intro to Git and GitHub |
Jun. 7, 2023 |
10am to 11am |
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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