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Article: 6-10× pyrosequencing is a practical approach for whole prokaryote genome studies
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Title6-10× pyrosequencing is a practical approach for whole prokaryote genome studies
 
AuthorsLi, J1
Jiang, J1
Leung, FC1
 
KeywordsLow depth
Pyrosequencing
Simulation study
Whole genome sequencing
 
Issue Date2012
 
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/gene
 
CitationGene, 2012, v. 494 n. 1, p. 57-64 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.gene.2011.11.051
 
AbstractNext 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. © 2011 Elsevier B.V.
 
ISSN0378-1119
2013 Impact Factor: 2.082
 
DOIhttp://dx.doi.org/10.1016/j.gene.2011.11.051
 
ISI Accession Number IDWOS:000300542800008
Funding AgencyGrant Number
Strategic Research Themes of Infection and Immunology and Initiatives of Clean Energy, University of Hong Kong
Funding Information:

This project was partially supported by the Strategic Research Themes of Infection and Immunology and Initiatives of Clean Energy, The University of Hong Kong. We are grateful to Dr. Andreas Tauch, Miao He and Brendan Wren for kindly providing the raw reads data from their projects.

 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorLi, J
 
dc.contributor.authorJiang, J
 
dc.contributor.authorLeung, FC
 
dc.date.accessioned2012-03-27T09:07:33Z
 
dc.date.available2012-03-27T09:07:33Z
 
dc.date.issued2012
 
dc.description.abstractNext 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. © 2011 Elsevier B.V.
 
dc.description.natureLink_to_subscribed_fulltext
 
dc.identifier.citationGene, 2012, v. 494 n. 1, p. 57-64 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.gene.2011.11.051
 
dc.identifier.citeulike10137301
 
dc.identifier.doihttp://dx.doi.org/10.1016/j.gene.2011.11.051
 
dc.identifier.epage64
 
dc.identifier.hkuros199087
 
dc.identifier.isiWOS:000300542800008
Funding AgencyGrant Number
Strategic Research Themes of Infection and Immunology and Initiatives of Clean Energy, University of Hong Kong
Funding Information:

This project was partially supported by the Strategic Research Themes of Infection and Immunology and Initiatives of Clean Energy, The University of Hong Kong. We are grateful to Dr. Andreas Tauch, Miao He and Brendan Wren for kindly providing the raw reads data from their projects.

 
dc.identifier.issn0378-1119
2013 Impact Factor: 2.082
 
dc.identifier.issue1
 
dc.identifier.pmid22192914
 
dc.identifier.scopuseid_2-s2.0-84856101175
 
dc.identifier.spage57
 
dc.identifier.urihttp://hdl.handle.net/10722/146038
 
dc.identifier.volume494
 
dc.languageeng
 
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/gene
 
dc.publisher.placeNetherlands
 
dc.relation.ispartofGene
 
dc.relation.referencesReferences in Scopus
 
dc.subject.meshGenome
 
dc.subject.meshProkaryotic Cells
 
dc.subject.meshSequence Analysis, DNA - methods
 
dc.subjectLow depth
 
dc.subjectPyrosequencing
 
dc.subjectSimulation study
 
dc.subjectWhole genome sequencing
 
dc.title6-10× pyrosequencing is a practical approach for whole prokaryote genome studies
 
dc.typeArticle
 
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Author Affiliations
  1. The University of Hong Kong