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dc.contributor.authorHuddleston, J.en_US
dc.contributor.authorRanade, S.en_US
dc.contributor.authorMalig, M.en_US
dc.contributor.authorAntonacci, F.en_US
dc.contributor.authorChaisson, M.en_US
dc.contributor.authorHon, L.en_US
dc.contributor.authorSudmant, P. H.en_US
dc.contributor.authorAlkan C.en_US
dc.contributor.authorEichler, E. E.en_US
dc.contributor.authorGraves, T. A.en_US
dc.contributor.authorDennis, M. Y.en_US
dc.contributor.authorWilson, R. K.en_US
dc.contributor.authorTurner, S. W.en_US
dc.contributor.authorKorlach, J.en_US
dc.date.accessioned2015-07-28T12:02:41Z
dc.date.available2015-07-28T12:02:41Z
dc.date.issued2014en_US
dc.identifier.issn1088-9051
dc.identifier.urihttp://hdl.handle.net/11693/12706
dc.description.abstractObtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger shotgun sequencing of clone inserts, however, has now been largely abandoned, leaving most of these regions unresolved in newer genome assemblies generated primarily by next-generation sequencing hybrid approaches. Here we show that it is possible to resolve regions that are complex in a genome-wide context but simple in isolation for a fraction of the time and cost of traditional methods using long-read single molecule, real-time (SMRT) sequencing and assembly technology from Pacific Biosciences (PacBio). We sequenced and assembled BAC clones corresponding to a 1.3-Mbp complex region of chromosome 17q21.31, demonstrating 99.994% identity to Sanger assemblies of the same clones. We targeted 44 differences using Illumina sequencing and find that PacBio and Sanger assemblies share a comparable number of validated variants, albeit with different sequence context biases. Finally, we targeted a poorly assembled 766-kbp duplicated region of the chimpanzee genome and resolved the structure and organization for a fraction of the cost and time of traditional finishing approaches. Our data suggest a straightforward path for upgrading genomes to a higher quality finished state.en_US
dc.language.isoEnglishen_US
dc.source.titleGenome Researchen_US
dc.relation.isversionofhttp://dx.doi.org/10.1101/gr.168450.113en_US
dc.subjectSegmental duplicationen_US
dc.subjectAssemblyen_US
dc.subjectPacBioen_US
dc.subjectSangeren_US
dc.subjectCapillaryen_US
dc.subjectAssembling complex genomic regions with long readsen_US
dc.titleReconstructing complex regions of genomes using long-read sequencing technologyen_US
dc.typeArticleen_US
dc.departmentDepartment of Computer Engineeringen_US
dc.citation.spage1en_US
dc.citation.epage23en_US
dc.identifier.doi10.1101/gr.168450.113en_US
dc.publisherCold Spring Harbor Laboratory Pressen_US
dc.identifier.eissn1549-5469


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