Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.

ABSTRACT:

Background

There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats.

Methodology/principal findings

Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a q

SUBMITTER: Cahill MJ 

PROVIDER: S-EPMC2902515 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature