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Bioinformatics Advance Access published online on June 19, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp377
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

Bas E. Dutilh 1,*, Martijn A. Huynen 1 and Marc Strous 2

1Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
2Department of Microbiology, Radboud University Nijmegen, Heyendaalsweg 135, 6525 AJ, Nijmegen, The Netherlands; MPI for Marine Microbiology, Celsiusstr. 1 D-28359, Bremen, Germany; Centre for Biotechnology, University of Bielefeld, Germany

*To whom correspondence should be addressed. Mr. Bas Dutilh, E-mail: dutilh{at}cmbi.ru.nl


  Abstract

Motivation: Most microbial species can not be cultured in the lab. Metagenomic sequencing may still yield a complete genome if the sequenced community is enriched and the sequencing coverage is high. However, the complexity in a natural population may cause the enrichment culture to contain multiple related strains. This diversity can confound existing strict assembly programs and lead to a fragmented assembly, which is unnecessary if we have a related reference genome available that can function as a scaffold. Results: Here, we map short metagenomic sequencing reads from a population of strains to a related reference genome, and compose a genome that captures the consensus of the population's sequences. We show that by iteration of the mapping and assembly procedure, the coverage increases while the similarity with the reference genome decreases. This indicates that the assembly becomes less dependent on the reference genome and approaches the consensus genome of the multi-strain population. Contact: dutilh{at}cmbi.ru.nl.

Associate Editor: Dr. Alex Bateman

Received on April 27, 2009; revised on June 12, 2009; accepted on June 15, 2009

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