title: REAPR: a universal tool for genome assembly evaluation.
abstract: Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/.
authors.forename: Martin
authors.initials: M
authors.lastname: Hunt
authors.forename: Taisei
authors.initials: T
authors.lastname: Kikuchi
authors.forename: Mandy
authors.initials: M
authors.lastname: Sanders
authors.forename: Chris
authors.initials: C
authors.lastname: Newbold
authors.forename: Matthew
authors.initials: M
authors.lastname: Berriman
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Otto
mesh_terms: D000465:Algorithms; D000818:Animals; D001419:Bacteria / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D015233:Models, Statistical; D017422:Sequence Analysis, DNA