English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT

Released

Journal Article

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

MPS-Authors
/persons/resource/persons210804

Strous,  M.
Microbial Fitness Group, Max Planck Institute for Marine Microbiology, Max Planck Society;

External Ressource
No external resources are shared
Fulltext (public)

Stous9.pdf
(Publisher version), 393KB

Supplementary Material (public)
There is no public supplementary material available
Citation

Dutilh, B., Huynen, M., & Strous, M. (2009). Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics, 25(21), 2878-2881.


Cite as: http://hdl.handle.net/21.11116/0000-0001-CBAC-9
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.