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Article: Correcting short reads with high error rates for improved sequencing result

TitleCorrecting short reads with high error rates for improved sequencing result
Authors
KeywordsBioinformatics
Error correction
Sequence assembly
Short reads
Issue Date2009
PublisherInderscience Publishers. The Journal's web site is located at http://www.inderscience.com/ijbra
Citation
International Journal Of Bioinformatics Research And Applications, 2009, v. 5 n. 2, p. 224-237 How to Cite?
AbstractIn the sequencing process, reads of the sequence are generated, then assembled to form contigs. New technologies can produce reads faster with lower cost and higher coverage. However, these reads are shorter. With errors, short reads make the assembly step more difficult. Chaisson et al. (2004) proposed an algorithm to correct the reads prior to the assembly step. The result is not satisfactory when the error rate is high (e.g., ≥ 3%). We improve their approach to handle reads of higher error rates. Experimental results show that our approach is much more effective in correcting errors, producing contigs of higher quality. Copyright © 2009 Inderscience Enterprises Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/60601
ISSN
2015 SCImago Journal Rankings: 0.231
References

 

DC FieldValueLanguage
dc.contributor.authorWong, TKFen_HK
dc.contributor.authorLam, TWen_HK
dc.contributor.authorChan, PYen_HK
dc.contributor.authorYiu, SMen_HK
dc.date.accessioned2010-05-31T04:14:46Z-
dc.date.available2010-05-31T04:14:46Z-
dc.date.issued2009en_HK
dc.identifier.citationInternational Journal Of Bioinformatics Research And Applications, 2009, v. 5 n. 2, p. 224-237en_HK
dc.identifier.issn1744-5485en_HK
dc.identifier.urihttp://hdl.handle.net/10722/60601-
dc.description.abstractIn the sequencing process, reads of the sequence are generated, then assembled to form contigs. New technologies can produce reads faster with lower cost and higher coverage. However, these reads are shorter. With errors, short reads make the assembly step more difficult. Chaisson et al. (2004) proposed an algorithm to correct the reads prior to the assembly step. The result is not satisfactory when the error rate is high (e.g., ≥ 3%). We improve their approach to handle reads of higher error rates. Experimental results show that our approach is much more effective in correcting errors, producing contigs of higher quality. Copyright © 2009 Inderscience Enterprises Ltd.en_HK
dc.languageengen_HK
dc.publisherInderscience Publishers. The Journal's web site is located at http://www.inderscience.com/ijbraen_HK
dc.relation.ispartofInternational Journal of Bioinformatics Research and Applicationsen_HK
dc.rightsInternational Journal of Bioinformatics Research and Applications. Copyright © Inderscience Publishers.en_HK
dc.subjectBioinformaticsen_HK
dc.subjectError correctionen_HK
dc.subjectSequence assemblyen_HK
dc.subjectShort readsen_HK
dc.subject.meshAlgorithms-
dc.subject.meshComputational Biology - methods-
dc.subject.meshDNA - chemistry-
dc.subject.meshDatabases, Genetic-
dc.subject.meshSequence Analysis, DNA - methods-
dc.titleCorrecting short reads with high error rates for improved sequencing resulten_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1744-5485&volume=5&issue=2&spage=224&epage=237&date=2009&atitle=Correcting+short+reads+with+high+error+rates+for+improved+sequencing+resulten_HK
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1504/IJBRA.2009.024039en_HK
dc.identifier.pmid19324607-
dc.identifier.scopuseid_2-s2.0-63149150664en_HK
dc.identifier.hkuros163535en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-63149150664&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume5en_HK
dc.identifier.issue2en_HK
dc.identifier.spage224en_HK
dc.identifier.epage237en_HK
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWong, TKF=25423289800en_HK
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridChan, PY=26435793700en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.citeulike11928580-

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