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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/.

SUBMITTER: Hunt M

PROVIDER: S-EPMC3798757 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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REAPR: a universal tool for genome assembly evaluation.

Hunt Martin M Kikuchi Taisei T Sanders Mandy M Newbold Chris C Berriman Matthew M Otto Thomas D TD

Genome biology 20130527 5

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, ...[more]

PMID: 23710727

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