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

Cahill MJ, Köser CU, Ross NE, Archer JA - PLoS ONE (2010)

Bottom Line: Nonetheless, there is considerable variation amongst prokaryotes.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.

View Article: PubMed Central - PubMed

Affiliation: Department 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.

Show MeSH
Assessing the performance of a range of read lengths.The fraction of the 818 genomes that meet gap benchmarks as a function of read length was calculated. The benchmarks were 762, 384, 192, 96, and 48 repeat-induced gaps. For example, assuming reads of 150nt, 50% of the genomes can be assembled with fewer than 96 gaps.
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pone-0011518-g004: Assessing the performance of a range of read lengths.The fraction of the 818 genomes that meet gap benchmarks as a function of read length was calculated. The benchmarks were 762, 384, 192, 96, and 48 repeat-induced gaps. For example, assuming reads of 150nt, 50% of the genomes can be assembled with fewer than 96 gaps.

Mentions: In Figure 4, the proportion of the 818 genomes that would meet the various gap benchmarks as read length increases is depicted. For 75% of the genomes analysed, a read length of only 245nt is enough to produce assemblies with fewer than 96 repeat-induced gaps. Reads of 125 and 70nt are sufficient for the same percentage of genomes to meet the 192 and 384 gap benchmarks, respectively.


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

Cahill MJ, Köser CU, Ross NE, Archer JA - PLoS ONE (2010)

Assessing the performance of a range of read lengths.The fraction of the 818 genomes that meet gap benchmarks as a function of read length was calculated. The benchmarks were 762, 384, 192, 96, and 48 repeat-induced gaps. For example, assuming reads of 150nt, 50% of the genomes can be assembled with fewer than 96 gaps.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2902515&req=5

pone-0011518-g004: Assessing the performance of a range of read lengths.The fraction of the 818 genomes that meet gap benchmarks as a function of read length was calculated. The benchmarks were 762, 384, 192, 96, and 48 repeat-induced gaps. For example, assuming reads of 150nt, 50% of the genomes can be assembled with fewer than 96 gaps.
Mentions: In Figure 4, the proportion of the 818 genomes that would meet the various gap benchmarks as read length increases is depicted. For 75% of the genomes analysed, a read length of only 245nt is enough to produce assemblies with fewer than 96 repeat-induced gaps. Reads of 125 and 70nt are sufficient for the same percentage of genomes to meet the 192 and 384 gap benchmarks, respectively.

Bottom Line: Nonetheless, there is considerable variation amongst prokaryotes.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.

View Article: PubMed Central - PubMed

Affiliation: Department 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.

Show MeSH