misFinder is a tool for checking assembly errors by using a reference genome and alignments of paired-end reads. Inconsistencies such as structural variant differences between draft assemblies and a reference genome (or closely related reference genome) help reveal assembly errors. In addition, unusual paired-end reads coverage and insert distance are also exploited to reveal potential assembly errors.
Zhu X, Leung HC, Wang R, Chin FY, Yiu SM, Quan G, Li Y, Zhang R, Jiang Q, Liu B, Dong Y, Zhou G, Wang Y "misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads." BMC Bioinformatics. 2015 Nov 16;16:386. https://doi.org/10.1186/s12859-015-0818-3
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