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dc.contributor.authorXin, H.en_US
dc.contributor.authorLee, D.en_US
dc.contributor.authorHormozdiari, F.en_US
dc.contributor.authorYedkar, S.en_US
dc.contributor.authorMutlu, O.en_US
dc.contributor.authorAlkan C.en_US
dc.date.accessioned2016-02-08T09:42:26Z
dc.date.available2016-02-08T09:42:26Z
dc.date.issued2013en_US
dc.identifier.issn1471-2164
dc.identifier.urihttp://hdl.handle.net/11693/21174
dc.description.abstractWith the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data. The success of all medical and genetic applications of next-generation sequencing critically depends on the existence of computational techniques that can process and analyze the enormous amount of sequence data quickly and accurately. Unfortunately, the current read mapping algorithms have difficulties in coping with the massive amounts of data generated by NGS. We propose a new algorithm, FastHASH, which drastically improves the performance of the seed-and-extend type hash table based read mapping algorithms, while maintaining the high sensitivity and comprehensiveness of such methods. FastHASH is a generic algorithm compatible with all seed-and-extend class read mapping algorithms. It introduces two main techniques, namely Adjacency Filtering, and Cheap K-mer Selection. We implemented FastHASH and merged it into the codebase of the popular read mapping program, mrFAST. Depending on the edit distance cutoffs, we observed up to 19-fold speedup while still maintaining 100% sensitivity and high comprehensiveness. © 2013 Xin et al.en_US
dc.language.isoEnglishen_US
dc.source.titleBMC Genomicsen_US
dc.relation.isversionofhttp://dx.doi.org/10.1186/1471-2164-14-S1-S13en_US
dc.subjectReference genomeen_US
dc.subjectTrue locationen_US
dc.subjectHash tableen_US
dc.subjectDynamic programming algorithmen_US
dc.subjectEdit distanceen_US
dc.titleAccelerating read mapping with FastHASHen_US
dc.typeArticleen_US
dc.departmentDepartment of Computer Engineeringen_US
dc.citation.spage1en_US
dc.citation.epage13en_US
dc.citation.volumeNumber14en_US
dc.identifier.doi10.1186/1471-2164-14-S1-S13en_US
dc.publisherBioMed Central Ltd.en_US


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