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PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked...
By LEGE 1002 days agogithub.com - PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It...Greengenes database
By Jit 3775 days agogreengenes.lbl.gov - The greengenes web application provides access to the 2011 version of the greengenes 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools presented by greengenes can assist the researcher in choosing...GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene...
By Rahul Nayak 2428 days agogithub.com - GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where...HiBC: Human Intestinal Bacteria Collection
By BioStar 541 days agoThe human gut is home to trillions of microorganisms, forming one of the most complex and dynamic microbial ecosystems known to science. The Human Intestinal Bacteria Collection (HiBC) is a pioneering initiative aimed at cataloging, preserving,...Snippy: Rapid haploid variant calling and core SNP phylogeny
By Neel 3002 days agogithub.com - Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is...BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data
By Neel 443 days agobakrep.computational.bio - 2,438,386 bacterial genomes at your fingertips consistently processed & characterized, enriched with metadata, accessible via a flexible search engine. BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data. It...MGRA: Breakpoint graphs and ancestral genome reconstructions
By Jit 3384 days ago Comments (1)http://mgra.cblab.org/ - MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes. It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and...Genomicus: genome browser that enables users to navigate in genomes in several dimensions
By Jit 3267 days agogenomicus.biologie.ens.fr - Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it...Scripts for the analysis of HGT in genome sequence data.
By Jit 3256 days agogithub.com - Scripts for the analysis of HGT in genome sequence data
