Producing polished prokaryotic pangenomes with the Panaroo pipeline.
Bacteria
Clustering
Horizontal gene transfer
Pangenome
Prokaryote
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
22 07 2020
22 07 2020
Historique:
received:
31
01
2020
accepted:
02
07
2020
entrez:
24
7
2020
pubmed:
24
7
2020
medline:
8
7
2021
Statut:
epublish
Résumé
Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here, we introduce Panaroo, a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. Panaroo is available at https://github.com/gtonkinhill/panaroo .
Identifiants
pubmed: 32698896
doi: 10.1186/s13059-020-02090-4
pii: 10.1186/s13059-020-02090-4
pmc: PMC7376924
doi:
Types de publication
Comparative Study
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
180Subventions
Organisme : Wellcome Trust
ID : 206194
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 107032/Z/15/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 204016
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom
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