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Database Syst."],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:p>Over the last decade, the cost of producing genomic sequences has dropped dramatically due to the current so-called next-generation sequencing methods. However, these next-generation sequencing methods are critically dependent on fast and sophisticated data processing methods for aligning a set of query sequences to a reference genome using rich string matching models. The focus of this work is on the design, development and evaluation of a data processing system for this crucial \u201cshort read alignment\u201d problem. Our system, called WHAM, employs hash-based indexing methods and bitwise operations for sequence alignments. It allows rich match models and it is significantly faster than the existing state-of-the-art methods. In addition, its relative speedup over the existing method is poised to increase in the future in which read sequence lengths will increase.<\/jats:p>","DOI":"10.1145\/2389241.2389247","type":"journal-article","created":{"date-parts":[[2013,1,2]],"date-time":"2013-01-02T13:23:15Z","timestamp":1357132995000},"page":"1-39","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":15,"title":["WHAM"],"prefix":"10.1145","volume":"37","author":[{"given":"Yinan","family":"Li","sequence":"first","affiliation":[{"name":"University of Wisconsin--Madison"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jignesh M.","family":"Patel","sequence":"additional","affiliation":[{"name":"University of Wisconsin--Madison"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Allison","family":"Terrell","sequence":"additional","affiliation":[{"name":"University of Wisconsin--Madison"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2012,12]]},"reference":[{"key":"e_1_2_1_1_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"volume-title":"Proceedings of the International Conference on Very Large Databases. 918--929","author":"Arasu A.","key":"e_1_2_1_2_1"},{"key":"e_1_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1145\/135239.135243"},{"key":"e_1_2_1_4_1","doi-asserted-by":"publisher","DOI":"10.1007\/PL00009253"},{"key":"e_1_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/0020-0190(96)00083-X"},{"key":"e_1_2_1_6_1","unstructured":"Burrows M. and Wheeler D. 1994. 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