Misassembly Detection using Paired-End Sequence Reads and Optical Mapping Data

TL;DR

This paper presents a new method that uses paired-end sequencing and optical mapping data to identify and correct misassemblies in draft genomes, improving genome assembly accuracy.

Contribution

The authors develop MISSEQUEL, a novel approach combining sequencing and optical mapping data to detect and remove misassemblies in genome drafts.

Findings

Detects over 54% of misassembled contigs in Francisella tularensis

Identifies between 31% and 100% of misassemblies in loblolly pine genomes

Enhances draft genome quality through integrated data analysis

Abstract

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/.