July 2022 Newsletter
Our July newsletter includes twenty two 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 webform:
https://biogrids.org/help/?tab=software
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.
MacOS 10.15 Catalina
Due to new security measures in OSX, installation under MacOS 10.15 requires an additional step. We have detailed a workaround to install BioGrids and SBGrid on new machines. Two approaches are available.
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 530 bioinfomatics 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 2.5.12
Linux: Installation Manager 2.5.12
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
demuxlet Genetic multiplexing of barcoded single cell RNA-seq.
Updated versions:f5044eb | Linux 64
cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Updated versions:4.1 | Linux 64 4.1 | OS X INTEL
UPIMAPI (UniProt Id Mapping through API) a command line interface for using UniProt's API, which allows access to UniProt's ID mapping programmatically.
Updated versions:1.8.2 | Linux 64 1.8.2 | OS X INTEL
hichipper is an open-source command-line toolkit that performs restriction fragment bias-aware preprocessing of HiChIP data.
Updated versions:0.7.7 | OS X INTEL 0.7.7 | Linux 64
clustalo is the latest version of Clustal: a multiple sequence alignment program for DNA or proteins.
Updated versions:1.2.4 | Linux 64 1.2.4 | OS X INTEL
BEAGLE is a software package for phasing genotypes and imputing ungenotyped markers.
Updated versions:5.4 | Linux 64 5.4 | OS X INTEL
Nextalign Viral genome sequence alignment tool
Updated versions:2.3.0 | Linux 64 2.3.0 | OS X INTEL
nextclade SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
Updated versions: 2.3.0 | Linux 64 2.3.0 | OS X INTEL
mega2 (Manipulation Environment for Genetic Analyses) - data-handling program for facilitating genetic linkage and association analyses.
Updated versions:6.0.0 | Linux 64 6.0.0 | OS X INTEL
pbsv PacBio structural variant (SV) calling and analysis tools
Updated versions:2.8.0 | Linux 64
lima is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data.
Updated versions:2.6.0 | Linux 64
shorah Short Reads Assembly into Haplotypes (ShoRAH) program for inferring viral haplotypes from NGS data
Updated versions:1.99.2 | OS X INTEL 1.99.2 | Linux 64
sourmash quickly searches, compares, and analyzes genomic and metagenomic data sets.
Updated versions:4.4.1 | Linux 64 4.4.1 | OS X INTEL
mentalist MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance.
Updated versions:0.2.4 | Linux 64
ivar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Updated versions:1.3.1 | OS X INTEL 1.3.1 | Linux 64
Entrez Edirect Utilities provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
Updated versions:16.2 | Linux 64 16.2 | OS X INTEL
htstream is a quality control and processing pipeline for High Throughput Sequencing data.
Updated versions:1.3.3 | OS X INTEL 1.3.3 | Linux 64
bcalm is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.
Updated versions:2.2.3 | OS X INTEL 2.2.3 | Linux 64
umap-learn (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction
Updated versions:0.5.3 | Linux 64
MultiQC aggregates results from bioinformatics analyses across many samples into a single report.
Updated versions:1.13a | Linux 64 1.13a | OS X INTEL
hatchet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.
Updated versions:1.0.1 | Linux 64 1.0.1 | OS X INTEL
HiCExplorer is a set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data.
Updated versions:3.7.2 | Linux 64 3.7.2 | OS X INTEL
Software Training
HMS Research Computing Spring 2022 sessions have ended.
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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