期刊
GENE
卷 494, 期 1, 页码 57-64出版社
ELSEVIER
DOI: 10.1016/j.gene.2011.11.051
关键词
Low depth; Pyrosequencing; Whole genome sequencing; Simulation study
资金
- Strategic Research Themes of Infection and Immunology and Initiatives of Clean Energy, University of Hong Kong
Next generation 454 pyrosequencing technology for whole bacterial genome sequencing involves a deep sequencing strategy with at least 15-20 x in depth proposed by official protocols but usually done with over 20 x in practices. In this study, we carried out a comprehensive evaluation of quality of the de novo assemblies based on realistic pyrosequencing simulated data from 1480 prokaryote genomes and 7 runs of machine-generated data. Our results demonstrated that for most of the prokaryote genomes, 6-10 x sequencing in qualified runs with 400 bp reads could produce high quality draft assembly (>98% genome coverage, <100 contigs with N50 size >100 kb, single base accuracy >99.99, indel error rate <0.01%, false gene loss/duplication rate <0.5%). Our study proves the power of low depth pyrosequencing strategy, which provides a cost-effective way for sequencing whole prokaryote genomes in a short time and enables further studies in microbial population diversity and comparative genomics. (C) 2011 Elsevier B.V All rights reserved.
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