Work

REAPR: a universal tool for genome assembly evaluation

Year: 2013

Type: article

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/.

Source: Genome biology

DOI: 10.1186/gb-2013-14-5-r47

Authors: Martin Hunt, Taisei Kikuchi, Mandy Sanders, Chris Newbold, Matthew Berriman, Thomas D Otto

Institutions: Wellcome Sanger Institute, University of Miyazaki, John Radcliffe Hospital, University of Oxford

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,490

Funders: Wellcome Trust, European Commission, Japan Society for the Promotion of Science