REAPR: a universal tool for genome assembly evaluation.
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 hav...
Main Authors: | , , , , , |
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Format: | Journal article |
Language: | English |
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2013
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author | Hunt, M Kikuchi, T Sanders, M Newbold, C Berriman, M Otto, T |
author_facet | Hunt, M Kikuchi, T Sanders, M Newbold, C Berriman, M Otto, T |
author_sort | Hunt, M |
collection | OXFORD |
description | 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/. |
first_indexed | 2024-03-07T00:59:51Z |
format | Journal article |
id | oxford-uuid:895585a4-961e-488a-8642-5b23cfcd46e4 |
institution | University of Oxford |
language | English |
last_indexed | 2024-03-07T00:59:51Z |
publishDate | 2013 |
record_format | dspace |
spelling | oxford-uuid:895585a4-961e-488a-8642-5b23cfcd46e42022-03-26T22:23:50ZREAPR: a universal tool for genome assembly evaluation.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:895585a4-961e-488a-8642-5b23cfcd46e4EnglishSymplectic Elements at Oxford2013Hunt, MKikuchi, TSanders, MNewbold, CBerriman, MOtto, TMethods 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/. |
spellingShingle | Hunt, M Kikuchi, T Sanders, M Newbold, C Berriman, M Otto, T REAPR: a universal tool for genome assembly evaluation. |
title | REAPR: a universal tool for genome assembly evaluation. |
title_full | REAPR: a universal tool for genome assembly evaluation. |
title_fullStr | REAPR: a universal tool for genome assembly evaluation. |
title_full_unstemmed | REAPR: a universal tool for genome assembly evaluation. |
title_short | REAPR: a universal tool for genome assembly evaluation. |
title_sort | reapr a universal tool for genome assembly evaluation |
work_keys_str_mv | AT huntm reaprauniversaltoolforgenomeassemblyevaluation AT kikuchit reaprauniversaltoolforgenomeassemblyevaluation AT sandersm reaprauniversaltoolforgenomeassemblyevaluation AT newboldc reaprauniversaltoolforgenomeassemblyevaluation AT berrimanm reaprauniversaltoolforgenomeassemblyevaluation AT ottot reaprauniversaltoolforgenomeassemblyevaluation |