Year: 2020
Type: article
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 .
Source: Genome biology
Institutions: University of Oslo, Wellcome Sanger Institute, University of Cambridge, MRC Laboratory of Molecular Biology, Molecular Immunity Unit, Medical Research Council, European Bioinformatics Institute, Imperial College London, Royal Papworth Hospital, Microsoft (United States), London School of Hygiene & Tropical Medicine, University of Helsinki, Helsinki Institute for Information Technology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $4,990
Awards: G1052272520, G1210355066, G127891921, G2347075150, MRC Centre for Global Infectious Disease Analysis, G3166327464, G3174639497, The host response to Staphylococcus aureus infection., Scalable inference algorithms for Bayesian evolutionary epidemiology, G6520098237, G6868616705, G7063735130, University of Cambridge - Mathematical Genomics and Medicine, Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers., G7659600897
OpenAlex ID: W3045244624