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Open Access Method

Detection and correction of false segmental duplications caused by genome mis-assembly

David R Kelley* and Steven L Salzberg

Author Affiliations

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA

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Genome Biology 2010, 11:R28  doi:10.1186/gb-2010-11-3-r28

Published: 10 March 2010

Abstract

Diploid genomes with divergent chromosomes present special problems for assembly software as two copies of especially polymorphic regions may be mistakenly constructed, creating the appearance of a recent segmental duplication. We developed a method for identifying such false duplications and applied it to four vertebrate genomes. For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes.