Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies

被引:29
作者
Cahill, Matt J. [1 ]
Koser, Claudio U. [1 ]
Ross, Nicholas E. [2 ]
Archer, John A. C. [3 ]
机构
[1] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England
[2] Univ Cambridge, Dept Chem Engn & Biotechnol, Cambridge CB2 3EH, England
[3] King Abdullah Univ Sci & Technol, Computat Biosci Res Ctr, Div Chem & Biol Engn, Thuwal, Saudi Arabia
来源
PLOS ONE | 2010年 / 5卷 / 07期
关键词
BACTERIAL GENOMES; ALGORITHMS; ALIGNMENT; GENETICS; IMPACT;
D O I
10.1371/journal.pone.0011518
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
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页数:9
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