Detection and correction of false segmental duplications caused by genome mis-assembly
Kelley, David R
Salzberg, Steven L
Kelley and Salzberg Genome Biology 2010, 11:R28 http://genomebiology.com/2010/11/3/R28
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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.