REAPR: a universal tool for genome assembly evaluation.

Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M. and Otto, T. D. (2013) REAPR: a universal tool for genome assembly evaluation. Genome Biology, 14(5), R47. (doi: 10.1186/gb-2013-14-5-r47) (PMID:22678431) (PMCID:PMC3648784)

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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/.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M., and Otto, T. D.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Genome Biology
Publisher:BioMed Central
ISSN:1474-760X
ISSN (Online):465-6906
Copyright Holders:Copyright © 2013 The Authors
First Published:First published in Genome Biology 14(5):R47
Publisher Policy:Reproduced under a Creative Commons License

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