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 |
| Published: |
2013
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| _version_ | 1797080424205254656 |
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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 |