Assisted assembly: How to improve a de novo genome assembly by using related species

Abstract

We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting process via a related genome. We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly. © 2009 Gnerre et al.; licensee BioMed Central Ltd.