6-10× pyrosequencing is a practical approach for whole prokaryote genome studies

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journal

9 Scopus Citations
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Author(s)

  • Jun Li
  • Jingwei Jiang
  • Frederick C. Leung

Detail(s)

Original languageEnglish
Pages (from-to)57-64
Journal / PublicationGene
Volume494
Issue number1
Online published13 Dec 2011
Publication statusPublished - 15 Feb 2012
Externally publishedYes

Abstract

Next generation 454 pyrosequencing technology for whole bacterial genome sequencing involves a deep sequencing strategy with at least 15-20 × in depth proposed by official protocols but usually done with over 20 × 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 × 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.  

Research Area(s)

  • Low depth, Pyrosequencing, Simulation study, Whole genome sequencing

Citation Format(s)

6-10× pyrosequencing is a practical approach for whole prokaryote genome studies. / Li, Jun; Jiang, Jingwei; Leung, Frederick C.

In: Gene, Vol. 494, No. 1, 15.02.2012, p. 57-64.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journal