  A crucial problem in genome assembly is the discovery and correction of
misassembly errors in draft genomes. We develop a method that will enhance the
quality of draft genomes by identifying and removing misassembly errors using
paired short read sequence data and optical mapping data. We apply our method
to various assemblies of the loblolly pine and Francisella tularensis genomes.
Our results demonstrate that we detect more than 54% of extensively
misassembled contigs and more than 60% of locally misassembed contigs in an
assembly of Francisella tularensis, and between 31% and 100% of extensively
misassembled contigs and between 57% and 73% of locally misassembed contigs in
the assemblies of loblolly pine. MISSEQUEL can be downloaded at
http://www.cs.colostate.edu/seq/.
