Producing polished prokaryotic pangenomes with the Panaroo pipeline.
Published version
Peer-reviewed
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Repository DOI
Change log
Authors
Tonkin-Hill, Gerry https://orcid.org/0000-0003-4397-2224
MacAlasdair, Neil
Ruis, Christopher
Weimann, Aaron
Horesh, Gal
Abstract
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 .
Description
Keywords
Bacteria, Clustering, Horizontal gene transfer, Pangenome, Prokaryote, Algorithms, Biological Evolution, Drug Resistance, Bacterial, Genome, Bacterial, Genomics, Klebsiella pneumoniae, Mycobacterium tuberculosis, Software
Journal Title
Genome Biol
Conference Name
Journal ISSN
1474-7596
1474-760X
1474-760X
Volume Title
21
Publisher
Springer Science and Business Media LLC
Publisher DOI
Sponsorship
Fondation Botnar (Project 603)
Wellcome Trust (107032/Z/15/Z)
Wellcome Trust (204016/Z/16/Z)
Cystic Fibrosis Trust (IH 001)
Wellcome Trust (107032/Z/15/Z)
Wellcome Trust (204016/Z/16/Z)
Cystic Fibrosis Trust (IH 001)