Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping

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dc.citation.epage1560en_US
dc.citation.issueNumber10en_US
dc.citation.spage1553en_US
dc.citation.volumeNumber31en_US
dc.contributor.authorXin, H.en_US
dc.contributor.authorGreth, J.en_US
dc.contributor.authorEmmons, J.en_US
dc.contributor.authorPekhimenko, G.en_US
dc.contributor.authorKingsford, C.en_US
dc.contributor.authorAlkan C.en_US
dc.contributor.authorMutlu, O.en_US
dc.date.accessioned2016-02-08T10:43:14Z
dc.date.available2016-02-08T10:43:14Z
dc.date.issued2015en_US
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractMotivation: Calculating the edit-distance (i.e. minimum number of insertions, deletions and substitutions) between short DNA sequences is the primary task performed by seed-and-extend based mappers, which compare billions of sequences. In practice, only sequence pairs with a small edit-distance provide useful scientific data. However, the majority of sequence pairs analyzed by seed-and-extend based mappers differ by significantly more errors than what is typically allowed. Such error-abundant sequence pairs needlessly waste resources and severely hinder the performance of read mappers. Therefore, it is crucial to develop a fast and accurate filter that can rapidly and efficiently detect error-abundant string pairs and remove them from consideration before more computationally expensive methods are used. Results: We present a simple and efficient algorithm, Shifted Hamming Distance (SHD), which accelerates the alignment verification procedure in read mapping, by quickly filtering out error-abundant sequence pairs using bit-parallel and SIMD-parallel operations. SHD only filters string pairs that contain more errors than a user-defined threshold, making it fully comprehensive. It also maintains high accuracy with moderate error threshold (up to 5% of the string length) while achieving a 3-fold speedup over the best previous algorithm (Gene Myers's bit-vector algorithm). SHD is compatible with all mappers that perform sequence alignment for verification.en_US
dc.identifier.doi10.1093/bioinformatics/btu856en_US
dc.identifier.issn1367-4803
dc.identifier.urihttp://hdl.handle.net/11693/25347
dc.language.isoEnglishen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofhttp://dx.doi.org/10.1093/bioinformatics/btu856en_US
dc.source.titleBioinformaticsen_US
dc.titleShifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mappingen_US
dc.typeArticleen_US
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