July 2021 Newsletter
Our July newsletter includes thirty one new and updated software titles. A major R package update provides 790 new packages for R 3.6.2. This brings the total to 1,420 packages available in R 3.6.2 As a reminder, new software titles can be requested by sending email to help@biogrids.org or filling out our webform:
https://biogrids.org/help/?tab=software
New BioGrids Installation Manager
Our new graphical Installation Manager for macOS and Linux is now available for general use. You can find a quick link to download MacOS and Linux versions at the top of our wiki page:
https://biogrids.org/wiki/Home
We welcome any and all feedback from the community at help@biogrids.org.
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 460 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, v2.2.15, is now available for Linux and MacOS computers:
macOS: Installation Manager 2.2.15
Linux: Installation Manager 2.2.15
BioGrids CLI Quick Start
Start 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
fqtools An efficient FASTQ manipulation suite.
Versions:2.1 | OS X INTEL 2.1 | Linux 64
MutMap pipeline to identify causative mutations responsible for a phenotype. Implements bulked segregant analysis.
Versions:2.3.2 | OS X INTEL 2.3.2 | Linux 64
FastME provides distance algorithms to infer phylogenies.
Versions:2.1.6.1 | Linux 64 2.1.6.1 | OS X INTEL
fastq-scan reads a FASTQ from STDIN and outputs summary statistics (read lengths, per-read qualities, per-base qualities) in JSON format.
Versions:0.4.4 | OS X INTEL 0.4.4 | Linux 64
abPOA is an extended version of Partial Order Alignment (POA) that performs adaptive banded dynamic programming (DP) with an SIMD implementation.
Versions:1.2.5 | Linux 64 1.2.5 | OS X INTEL
srprism Short Read Alignment Tool
Versions:2.4.24 | OS X INTEL 2.4.24 | Linux 64
HULK is a tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.
Versions:1.0.0 | Linux 64 1.0.0 | OS X INTEL
skesa Strategic Kmer Extension for Scrupulous Assemblies
Versions:2.4.0 | Linux 64 2.4.0 | OS X INTEL
tn93 Compute pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.
Versions:1.0.6 | OS X INTEL 1.0.6 | Linux 64
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
Versions:1.32 | Linux 64 1.32 | OS X INTEL
Ococo the first program capable of inferring variants in a real-time, as read alignments are fed in.
Versions:0.1.2.4 | Linux 64 0.1.2.4 | OS X INTEL
PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.
Versions:v.170427 | OS X INTEL v.170427 | Linux 64
Daligner Find all significant local alignments between reads
Versions:1.0.20200322 | Linux 64 1.0.20200322 | OS X INTEL
dart a fast and accurate RNA-seq mapper with a divide and conquer strategy
Versions:1.4.6 | OS X INTEL 1.4.6 | Linux 64
scrm is a coalescent simulator for biological sequences
Versions:1.7.4 | Linux 64 1.7.4 | OS X INTEL
clark Fast, accurate and versatile k-mer based classification system
Versions:1.2.6.1 | OS X INTEL 1.2.6.1 | Linux 64
Lighter is a kmer-based error correction method for whole genome sequencing data.
Versions:1.1.2 | Linux 64 1.1.2 | OS X INTEL
snp-sites Rapidly extracts SNPs from a multi-FASTA alignment.
Versions:2.5.1 | OS X INTEL 2.5.1 | Linux 64
Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT).
Versions:0.4.1 | OS X INTEL 0.4.1 | Linux 64
RNA-SeQC Fast, efficient RNA-Seq metrics for quality control and process optimization
Versions:2.3.5 | Linux 64 2.3.5 | OS X INTEL
kallisto a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
Versions:0.46.2 | OS X INTEL 0.46.2 | Linux 64
FFmpeg a complete, cross-platform solution to record, convert and stream audio and video.
Versions:4.4 | Linux 64 4.4 | OS X INTEL
SAMtools (Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Versions:1.13 | Linux 64 OS X INTEL
Tracy basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
Versions:0.6.1 | OS X INTEL 0.6.1 | Linux 64
Filtlong is a tool for filtering long reads by quality.
Versions:0.2.1 | OS X INTEL 0.2.1 | Linux 64
Cuttlefish is a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from genome reference(s).
Versions:1.0.0 | Linux 64 1.0.0 | OS X INTEL
UShER a program that rapidly places new samples onto an existing phylogeny using maximum parsimony. It is particularly helpful in understanding the relationships of newly sequenced SARS-CoV-2 genomes with each other and with previously sequenced genomes in a global phylogeny.
Versions:0.3.5 | Linux 64 0.3.5 | OS X INTEL
Subread comprises a suite of software programs for processing next-gen sequencing read data.
Versions:2.0.3 | Linux 64 2.0.3 | OS X INTEL
UMI-tools Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
Versions:1.1.2 | OS X INTEL 1.1.2 | Linux 64
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Versions: R 3.6.2 and R 4.0.2
Salmon a tool for quantifying the expression of transcripts using RNA-seq data.
Versions:1.5.1 | Linux 64 1.5.1 | OS X INTEL
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Summer training courses have ended. Please see the HMS Research Computing Training Portal for the most current updates.
The Harvard Chan Bioinformatics Core
Courses for Summer 2021 are now open. See the Workshop Updates page for updates.
| Topic |
Category |
Date |
Duration |
Prerequisites |
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| Command-line Interface (Shell) and HPC |
Basic |
August 17th, 20th & 24th |
Three 2.5h sessions |
-- |
ChIP-seq Part 1
(Experimental design to Peak calling) |
Advanced |
September 21st, 24th & 28th |
Three 2.5h sessions |
Shell |
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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