Producing polished prokaryotic pangenomes with the Panaroo pipeline

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…

• WT
  Wellcome Trust

  Awards: 107032/Z/15/Z, /Z/15/Z, 206194
• CF
  Cystic Fibrosis Trust

  Award: IH001
• EC
  European Commission

  Awards: EDCTP2, MR/R015600/1, 742158, EDCTP2 programme
• DF
  Department for International Development

  Award: MR/R015600/1
• FB
  Fondation Botnar
• MR
  Medical Research Council

  Awards: MR/R015600/1, MR/R015600/1
• EA
  European and Developing Countries Clinical Trials Partnership

  Awards: MR/R015600/1, EDCTP2