MAGNET: understanding and improving the accuracy of genome pre-alignment filtering

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dc.citation.epage10en_US
dc.citation.issueNumber2en_US
dc.citation.spage1en_US
dc.citation.volumeNumber13en_US
dc.contributor.authorAlser, M.en_US
dc.contributor.authorMutlu, O.en_US
dc.contributor.authorAlkan C.en_US
dc.date.accessioned2019-02-13T10:45:05Z
dc.date.available2019-02-13T10:45:05Z
dc.date.issued2017en_US
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractIn the era of high throughput DNA sequencing (HTS) technologies, calculating the edit distance (i.e.,the minimum number of substitutions, insertions, and deletionsbetween a pair of sequences) forbillions of genomicsequences is the computational bottleneck intoday’s read mappers. The shifted Hamming distance (SHD) algorithm proposes afast filtering strategy that can rapidly filter out invalid mappings that have more edits than allowed. However, SHD shows high inaccuracy in its filtering by admitting invalid mappings to be marked as correct ones. This wastesthe execution time and imposesa large computational burden. In this work, we comprehensively investigate foursources that lead to the filtering inaccuracy. We propose MAGNET, anewfiltering strategy that maintains high accuracy across different edit distance thresholds and data sets. It significantly improvestheaccuracy of pre-alignment filtering by one to twoordersof magnitude.The MATLAB implementationsof MAGNETand SHDareopen source and available at:https://github.com/BilkentCompGen/MAGNET.en_US
dc.description.provenanceSubmitted by Türkan Cesur (cturkan@bilkent.edu.tr) on 2019-02-13T10:45:05Z No. of bitstreams: 1 MAGNET understanding_and_improvingthe_accuracy_of_genome_pre-alignment_filtering.pdf: 788809 bytes, checksum: 3667ca7aa3652d433e2ec698fdad7696 (MD5)en
dc.description.provenanceMade available in DSpace on 2019-02-13T10:45:05Z (GMT). No. of bitstreams: 1 MAGNET understanding_and_improvingthe_accuracy_of_genome_pre-alignment_filtering.pdf: 788809 bytes, checksum: 3667ca7aa3652d433e2ec698fdad7696 (MD5) Previous issue date: 2017en
dc.identifier.issn1820-4503
dc.identifier.urihttp://hdl.handle.net/11693/49418
dc.language.isoEnglishen_US
dc.publisherI P S Ien_US
dc.source.titleTransactions on Internet Researchen_US
dc.subjectHigh throughput DNA sequencingen_US
dc.subjectRead mappingen_US
dc.subjectRead alignmenten_US
dc.subjectFalse positivesen_US
dc.titleMAGNET: understanding and improving the accuracy of genome pre-alignment filteringen_US
dc.typeArticleen_US

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