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dc.contributor.authorAllam, Amin
dc.contributor.authorKalnis, Panos
dc.contributor.authorSolovyev, Victor
dc.date.accessioned2015-08-17T08:21:19Z
dc.date.available2015-08-17T08:21:19Z
dc.date.issued2015-07-14
dc.identifier.citationKarect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data 2015:btv415 Bioinformatics
dc.identifier.issn1367-4803
dc.identifier.issn1460-2059
dc.identifier.pmid26177965
dc.identifier.doi10.1093/bioinformatics/btv415
dc.identifier.urihttp://hdl.handle.net/10754/567063
dc.description.abstractMotivation: Next-generation sequencing generates large amounts of data affected by errors in the form of substitutions, insertions or deletions of bases. Error correction based on the high-coverage information, typically improves de novo assembly. Most existing tools can correct substitution errors only; some support insertions and deletions, but accuracy in many cases is low. Results: We present Karect, a novel error correction technique based on multiple alignment. Our approach supports substitution, insertion and deletion errors. It can handle non-uniform coverage as well as moderately covered areas of the sequenced genome. Experiments with data from Illumina, 454 FLX and Ion Torrent sequencing machines demonstrate that Karect is more accurate than previous methods, both in terms of correcting individual-bases errors (up to 10% increase in accuracy gain) and post de novo assembly quality (up to 10% increase in NGA50). We also introduce an improved framework for evaluating the quality of error correction.
dc.language.isoen
dc.publisherOxford University Press (OUP)
dc.relation.urlhttp://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/bioinformatics/btv415
dc.rightsThis is a pre-copyedited, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The version of record Allam, Amin, Panos Kalnis, and Victor Solovyev. "Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data." Bioinformatics (2015): btv415. is available online at: http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/bioinformatics/btv415.
dc.titleKarect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalBioinformatics
dc.eprint.versionPost-print
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personAllam, Amin
kaust.personKalnis, Panos
kaust.personSolovyev, Victor
refterms.dateFOA2016-07-14T00:00:00Z
dc.date.published-online2015-07-14
dc.date.published-print2015-11-01


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