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

Title6-10× pyrosequencing is a practical approach for whole prokaryote genome studies
Authors
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
Citation
Gene, 2012, v. 494 n. 1, p. 57-64 How to Cite?
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.
Persistent Identifierhttp://hdl.handle.net/10722/146038
ISSN
2014 Impact Factor: 2.138
ISI Accession Number ID
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.

References

 

DC FieldValueLanguage
dc.contributor.authorLi, Jen_HK
dc.contributor.authorJiang, Jen_HK
dc.contributor.authorLeung, FCen_HK
dc.date.accessioned2012-03-27T09:07:33Z-
dc.date.available2012-03-27T09:07:33Z-
dc.date.issued2012en_HK
dc.identifier.citationGene, 2012, v. 494 n. 1, p. 57-64en_HK
dc.identifier.issn0378-1119en_HK
dc.identifier.urihttp://hdl.handle.net/10722/146038-
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.en_HK
dc.languageengen_US
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/geneen_HK
dc.relation.ispartofGeneen_HK
dc.subjectLow depthen_HK
dc.subjectPyrosequencingen_HK
dc.subjectSimulation studyen_HK
dc.subjectWhole genome sequencingen_HK
dc.subject.meshGenome-
dc.subject.meshProkaryotic Cells-
dc.subject.meshSequence Analysis, DNA - methods-
dc.title6-10× pyrosequencing is a practical approach for whole prokaryote genome studiesen_HK
dc.typeArticleen_HK
dc.identifier.emailLeung, FC: fcleung@hkucc.hku.hken_HK
dc.identifier.authorityLeung, FC=rp00731en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.gene.2011.11.051en_HK
dc.identifier.pmid22192914-
dc.identifier.scopuseid_2-s2.0-84856101175en_HK
dc.identifier.hkuros199087en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-84856101175&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume494en_HK
dc.identifier.issue1en_HK
dc.identifier.spage57en_HK
dc.identifier.epage64en_HK
dc.identifier.isiWOS:000300542800008-
dc.publisher.placeNetherlandsen_HK
dc.identifier.scopusauthoridLi, J=54881403300en_HK
dc.identifier.scopusauthoridJiang, J=37085887400en_HK
dc.identifier.scopusauthoridLeung, FC=7103078633en_HK
dc.identifier.citeulike10137301-

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