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

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, t

SUBMITTER: Dutilh BE 

PROVIDER: S-EPMC2781756 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature