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dc.contributor.authorLee, D.en_US
dc.contributor.authorHormozdiari, F.en_US
dc.contributor.authorXin, H.en_US
dc.contributor.authorHach, F.en_US
dc.contributor.authorMutlu, O.en_US
dc.contributor.authorAlkan C.en_US
dc.date.accessioned2016-02-08T10:05:02Z
dc.date.available2016-02-08T10:05:02Z
dc.date.issued2015en_US
dc.identifier.issn1046-2023
dc.identifier.urihttp://hdl.handle.net/11693/22814
dc.description.abstractMany recent advances in genomics and the expectations of personalized medicine are made possible thanks to power of high throughput sequencing (HTS) in sequencing large collections of human genomes. There are tens of different sequencing technologies currently available, and each HTS platform have different strengths and biases. This diversity both makes it possible to use different technologies to correct for shortcomings; but also requires to develop different algorithms for each platform due to the differences in data types and error models. The first problem to tackle in analyzing HTS data for resequencing applications is the read mapping stage, where many tools have been developed for the most popular HTS methods, but publicly available and open source aligners are still lacking for the Complete Genomics (CG) platform. Unfortunately, Burrows-Wheeler based methods are not practical for CG data due to the gapped nature of the reads generated by this method. Here we provide a sensitive read mapper (sirFAST) for the CG technology based on the seed-and-extend paradigm that can quickly map CG reads to a reference genome. We evaluate the performance and accuracy of sirFAST using both simulated and publicly available real data sets, showing high precision and recall rates.en_US
dc.language.isoEnglishen_US
dc.source.titleMethodsen_US
dc.relation.isversionofhttp://dx.doi.org/10.1016/j.ymeth.2014.10.012en_US
dc.subjectComplete genomicsen_US
dc.subjectGapped readsen_US
dc.subjectHigh throughput sequencingen_US
dc.subjectRead mappingen_US
dc.subjectDNAen_US
dc.subjectAccuracyen_US
dc.subjectControlled studyen_US
dc.subjectData analysis softwareen_US
dc.subjectDNA sequenceen_US
dc.subjectGene mappingen_US
dc.subjectGenetic algorithmen_US
dc.subjectGenomicsen_US
dc.subjectHigh throughput sequencingen_US
dc.subjectHumanen_US
dc.subjectHuman genomeen_US
dc.subjectIndel mutationen_US
dc.subjectPersonalized medicineen_US
dc.subjectPriority journalen_US
dc.subjectSensitivity and specificityen_US
dc.titleFast and accurate mapping of complete genomics readsen_US
dc.typeArticleen_US
dc.departmentDepartment of Computer Engineeringen_US
dc.citation.spage3en_US
dc.citation.epage10en_US
dc.citation.volumeNumber79-80en_US
dc.identifier.doi10.1016/j.ymeth.2014.10.012en_US
dc.publisherAcademic Pressen_US


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