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Bioinformatics. 2009 Nov 1;25(21):2878-81. doi: 10.1093/bioinformatics/btp377. Epub 2009 Jun 19.

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

Author information

  • 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, Germany. dutilh@cmbi.ru.nl

Abstract

MOTIVATION:

Most microbial species can not be cultured in the laboratory. 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@cmbi.ru.nl

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
19542148
[PubMed - indexed for MEDLINE]
PMCID:
PMC2781756
Free PMC Article

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