October 2024 Newsletter
Our October software updates include twenty 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
AlphaFold - an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions:2.3.2_20241024 | Linux 64
Luna - an open-source C/C++ software package for manipulating and analyzing polysomnographic recordings, with a focus on the sleep EEG.
Updated versions:1.0.0-lgbm | Linux 64
RBPBench - a multi-function tool to evaluate CLIP-seq and other genomic region data using a comprehensive collection of known RNA-binding protein (RBP) binding motifs.
Updated versions:1.0.1 | Linux 64 1.0.1 | OS X INTEL
DNAscent - a software designed to detect the base analogues BrdU and EdU in single molecules of DNA sequenced on the Oxford Nanopore platform
Updated versions:4.0.3 | Linux 64
gsMap - (genetically informed spatial mapping of cells for complex traits) integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS) summary statistics to map cells to human complex traits, including diseases, in a spatially resolved manner.
Updated versions:1.70 | Linux 64 1.70 | OS X INTEL
strobealign - a read mapper that is typically significantly faster than other read mappers while achieving comparable or better accuracy, see the performance evaluation.
Updated versions:0.14.0 | Linux 64 0.14.0 | OS X INTEL
LazyPredict - helps build a lot of basic models without much code and helps understand which models works better without any parameter tuning.
Updated versions:0.2.12 | OS X INTEL 0.2.12 | Linux 64
tidk - identify and find telomeres, or telomeric repeats in a genome.
Updated versions:0.2.63 | Linux 64 0.2.63 | OS X INTEL
LongReadSum - supports FASTA, FASTQ, BAM, FAST5, and sequencing_summary.txt file formats for quick generation of QC data in HTML and text format.
Updated versions:1.3.1 | OS X INTEL 1.3.1 | Linux 64
smoothxg - local reconstruction of variation graphs using partial order alignment. Pangenome graphs built from raw sets of alignments may have complex local structures generated by common patterns of genome variation. smoothxg can be used to extract the consensus pangenome graph by applying the heaviest bundle algorithm to each chain.
Updated versions:0.6.7 | Linux 64
falco - a drop-in C++ implementation of FastQC to assess the quality of sequence reads.
Updated versions:1.2.1 | Linux 64 1.2.1 | OS X INTEL
Recentrifuge - robust comparative analysis and contamination removal for metagenomics
Updated versions:1.13.1 | OS X INTEL 1.13.1 | Linux 64
epic2 - ultraperformant Chip-Seq broad domain finder based on SICER.
Updated versions:0.0.52 | Linux 64
hifiasm_meta - metagenome assembler for Hifi reads, based on hifiasm.
Updated versions:hamtv0.3.1 | OS X INTEL hamtv0.3.1 | Linux 64
panacus - a counting tool for pangenome graphs. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.
Updated versions:0.2.4 | Linux 64 0.2.4 | OS X INTEL
gappa - Genesis Applications for Phylogenetic Placement Analysis
Updated versions:0.8.5 | Linux 64 0.8.5 | OS X INTEL
VeryFastTree - a new tool designed for efficient phylogenetic tree inference, specifically tailored to handle massive taxonomic datasets. It is a highly-tuned implementation based on the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to speed up the inference of phylogenies for huge alignments.
Updated versions:4.0.4 | Linux 64 4.0.4 | OS X INTEL
Spark - a multi-language engine for executing data engineering, data science, and machine learning on single-node machines or clusters.
Updated versions:3.5.3 | Linux 64
covtobed - a tool to generate BED coverage tracks from BAM files. It reads one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range.
Updated versions:1.3.5 | Linux 64 1.3.5 | OS X INTEL
EPA-ng - a complete rewrite of the Evolutionary Placement Algorithm (EPA), previously implemented in RAxML. It uses libpll and pll-modules to perform maximum likelihood-based phylogenetic placement of genetic sequences on a user-supplied reference tree and alignment.
Updated versions:0.3.8 | Linux 64 0.3.8 | 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.
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