Assisted assembly: how to improve a de novo genome assembly by using related species
1 Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, Massachusetts 02142, USA
2 Department of Medical Biochemistry and Microbiology, Uppsala University, Husarg.3, Uppsala 751 23, Sweden
Genome Biology 2009, 10:R88 doi:10.1186/gb-2009-10-8-r88Published: 27 August 2009
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.