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

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

Blog Article

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 CHEST RUB/STOPITCOLD 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 Flat TV Screen Cleaner 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.