April 2024 Newsletter
Our software updates include 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 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
ProPhyle - is an accurate, resource-frugal and deterministic phylogeny-based metagenomic classifier.
Updated versions:0.3.3.2 | Linux 64 0.3.3.2 | OS X INTEL
Pangolin-DL - is a deep-learning based method for predicting splice site strengths.
Updated versions:1.0.1 | OS X INTEL 1.0.1 | Linux 64
HiCExplorer - is a set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data.
Updated versions:3.7.3 | Linux 64 3.7.3 | OS X INTEL
AWS CLI - (Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.
Updated versions:2.15.40 | Linux 64
goleft - is a collection of bioinformatics tools written in go distributed together as a single binary.
Updated versions:0.2.6 | Linux 64 0.2.6 | OS X INTEL
BCFtools - a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Updated versions:1.20 | Linux 64 1.20 | OS X INTEL
Cutadapt - finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Updated versions:4.8 | Linux 64 4.8 | OS X INTEL
breseq - a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes.
Updated versions:0.38.3 | Linux 64 0.38.3 | OS X INTEL
locarna - tools for the structural analysis of RNA.
Updated versions:2.0.0 | OS X INTEL 2.0.0 | Linux 64
Sniffles - a structural variation caller using third generation sequencing.
Updated versions:2.3.2 | Linux 64 2.3.2 | OS X INTEL
SeqFu - (Sequece Fastx Utilities) a general-purpose program to manipulate and parse information from FASTA/FASTQ files.
Updated versions:1.20.3 | Linux 64 1.20.3 | 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.
Updated versions:1.20 | Linux 64 1.20 | OS X INTEL
Balrog - a universal protein model for prokaryotic gene prediction.
Updated versions:0.5.1 | Linux 64 0.5.1 | 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:0.7.18 | Linux 64 0.7.18 | OS X INTEL
bamtofastq - tool for converting 10x BAMs produced by Cell Ranger
Updated versions:1.4.1 | OS X INTEL 1.4.1 | Linux 64
bfc - a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data.
Updated versions:r181 | Linux 64 r181 | OS X INTEL
Bismark - a set of tools for the time-efficient analysis of Bisulfite-Seq (BS-Seq) data. Bismark performs alignments of bisulfite-treated reads to a reference genome and cytosine methylation calls at the same time.
Updated versions:0.24.2 | Linux 64 0.24.2 | OS X INTEL
Ghostscript - an interpreter for the PostScript (TM) language. It can display and convert postscript files.
Updated versions:10.03.0 | Linux 64 10.03.0 | OS X INTEL
Foldseek - enables fast and sensitive comparisons of large structure sets.
Updated versions:8-ef4e960 | Linux 64 8-ef4e960 | OS X INTEL
Captus - Assembly of Phylogenomic Datasets from High-Throughput Sequencing data.
Updated versions:1.0.1 | Linux 64 1.0.1 | OS X INTEL
arcasHLA - high-resolution HLA typing from RNA seq.
Updated versions:0.6.0 | OS X INTEL 0.6.0 | Linux 64
Infernal - (INFERence of RNA ALignment) searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs).
Updated versions:1.1.5 | Linux 64 1.1.5_arm | OS X INTEL 1.1.5 | OS X INTEL
Flye - fast and accurate de novo assembler for single molecule sequencing reads.
Updated versions:2.9.3 | Linux 64 2.9.3 | 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.
|
|
|
|
|
