REAPR is a tool for reference-free evaluation of the quality of genome assembly. This tool uses paired reads to determine base accuracy and identify mis-assemblies. It reports error free bases and a new metric known as corrected N50.
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD "REAPR: a universal tool for genome assembly evaluation." Genome Biol. 2013 May 27;14(5):R47. https://doi.org/10.1186/gb-2013-14-5-r47
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