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

Sante Gnerre1*, Eric S Lander1, Kerstin Lindblad-Toh12 and David B Jaffe1

Author Affiliations

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

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Genome Biology 2009, 10:R88  doi:10.1186/gb-2009-10-8-r88

Published: 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.