Journal
GENOME BIOLOGY
Volume 14, Issue 5, Pages -Publisher
BMC
DOI: 10.1186/gb-2013-14-5-r47
Keywords
Genome assembly; validation; evaluation
Funding
- European Union
- Wellcome Trust [098051, 082130/Z/07/Z]
- JSPS KAKENHI [24780044]
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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/.
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