EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations.
EnteroBase
accessory genome
big data
cgMLST
genomic databases
hierarchical clustering
Journal
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
ISSN: 1471-2970
Titre abrégé: Philos Trans R Soc Lond B Biol Sci
Pays: England
ID NLM: 7503623
Informations de publication
Date de publication:
10 10 2022
10 10 2022
Historique:
entrez:
22
8
2022
pubmed:
23
8
2022
medline:
24
8
2022
Statut:
ppublish
Résumé
The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000s of genomes to the species/subspecies and population levels for
Identifiants
pubmed: 35989609
doi: 10.1098/rstb.2021.0240
pmc: PMC9393565
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
20210240Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 202792/Z/16/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 202792/Z/16/Z
Pays : United Kingdom
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