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


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.

SUBMITTER: Kelley DR 

PROVIDER: S-EPMC2864568 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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

Kelley David R DR   Salzberg Steven L SL  

Genome biology 20100310 3


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. ...[more]

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