Misassembly detection using paired-end sequence reads and optical mapping data.

ABSTRACT:

Motivation

A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method called misSEQuel that enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data. Our method also fulfills the critical need for open source computational methods for analyzing optical mapping data. We apply our method to various assemblies of the loblolly pine, Francisella tularensis, rice and budgerigar genomes. We generated and used stimulated optical mapping data for loblolly pine and F.tularensis and used real optical mapping data for rice and budgerigar.

Results

Our results demonstrate that we detect more than 54% of extensively misassembled

SUBMITTER: Muggli MD 

PROVIDER: S-EPMC4542784 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature