Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
PLoS One. 2010 Jul 12;5(7):e11518. doi: 10.1371/journal.pone.0011518.

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

Author information

  • 1Department of Genetics, University of Cambridge, Cambridge, United Kingdom.

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 quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads.

CONCLUSIONS:

Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length.

PMID:
20634954
[PubMed - indexed for MEDLINE]
PMCID:
PMC2902515
Free PMC Article

Images from this publication.See all images (6)Free text

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for Public Library of Science Icon for PubMed Central
    Loading ...
    Write to the Help Desk