{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/92977"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/92977","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Efficient parallelization of Bowtie 2 with OpenCL on GPU","abstract":"As a crucial and computation-intensive aspect in bioinformatics, sequence alignment has gained considerable attention from researchers and developers. Among all the sequence aligners, Bowtie 2 is one of the most commonly used, due to its high speed and accuracy. This thesis presents a parallel implementation of Bowtie 2 with OpenCL, which is a parallel programming model that is becoming widely known and receiving great interest from researchers in recent years. This OpenCL implementation has high portability on various devices, such as multi-core CPU, GPU, and FPGA. This thesis focuses on an efficient and accurate parallelization on GPU. Optimizations that can be accommodated to any devices have been applied, as well as GPU-related optimizations.","abstract_html":"As a crucial and computation-intensive aspect in bioinformatics, sequence alignment has gained considerable attention from researchers and developers. Among all the sequence aligners, Bowtie 2 is one of the most commonly used, due to its high speed and accuracy. This thesis presents a parallel implementation of Bowtie 2 with OpenCL, which is a parallel programming model that is becoming widely known and receiving great interest from researchers in recent years. This OpenCL implementation has high portability on various devices, such as multi-core CPU, GPU, and FPGA. This thesis focuses on an efficient and accurate parallelization on GPU. Optimizations that can be accommodated to any devices have been applied, as well as GPU-related optimizations.","abstract_has_math":false,"creators":["Yan, Yan"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Electrical & Computer Engr","degree_department":null,"school":null,"contributors":["Chen, Deming"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-11-10T18:35:35Z","date_published":"2016-11-10T18:35:35Z","updated_at":"2026-07-22T22:26:35Z","subjects":["OpenCL","Bowtie 2","Sequence Aligner","Smith-Waterman"],"languages":["en"],"rights":["Copyright 2016 Yan Yan"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/92977","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Chen, Deming"]},{"key":"dc:creator","label":"Author","values":["Yan, Yan"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2016-11-10T18:35:35Z","2018-11-11T10:15:36Z","2016-07-21","2016-08"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Electrical & Computer Engr"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["OpenCL","Bowtie 2","Sequence Aligner","Smith-Waterman"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2016 Yan Yan"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/92977"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["As a crucial and computation-intensive aspect in bioinformatics, sequence alignment has gained considerable attention from researchers and developers. 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