{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/95394"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/95394","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"FPGA acceleration of DNA error correction","abstract":"Correcting errors in DNA sequencing data is an important process that can improve the quality of downstream analyses using the data. Even though many error-correction methods have been proposed for Illumina reads, their throughput is not high enough to process data from large genomes. The thesis describes the first FPGA-based error-correction tool, which is designed to improve the throughput of DNA error correction for Illumina reads. The base algorithm of the FPGA implementation is BLESS which is highly accurate but slow. The hardware implemented on the FPGA consists of a Bloom filter that is the main data structure of BLESS and the error-correction subroutines in BLESS. The design is compared with the software version of BLESS, and two other leading tools. The results show significant improvements in speed for the FPGA-based implementation with comparable accuracy of error correction.","abstract_html":"Correcting errors in DNA sequencing data is an important process that can improve the quality of downstream analyses using the data. Even though many error-correction methods have been proposed for Illumina reads, their throughput is not high enough to process data from large genomes. The thesis describes the first FPGA-based error-correction tool, which is designed to improve the throughput of DNA error correction for Illumina reads. The base algorithm of the FPGA implementation is BLESS which is highly accurate but slow. The hardware implemented on the FPGA consists of a Bloom filter that is the main data structure of BLESS and the error-correction subroutines in BLESS. The design is compared with the software version of BLESS, and two other leading tools. The results show significant improvements in speed for the FPGA-based implementation with comparable accuracy of error correction.","abstract_has_math":false,"creators":["Ramachandran, Anand"],"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":2017,"date_issued":"2017-03-01T15:49:26Z","date_published":"2017-03-01T15:49:26Z","updated_at":"2026-07-22T22:26:37Z","subjects":["Field programmable gate arrays (FPGA)","Acceleration","Sequencing","DNA error correction"],"languages":["en"],"rights":["Copyright 2016 Anand Ramachandran"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/95394","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":["Ramachandran, Anand"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2017-03-01T15:49:26Z","2016-12-05","2016-12"]},{"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":["Field programmable gate arrays (FPGA)","Acceleration","Sequencing","DNA error correction"]}]},{"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 Anand Ramachandran"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/95394"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Correcting errors in DNA sequencing data is an important process that can improve the quality of downstream analyses using the data. Even though many error-correction methods have been proposed for Illumina reads, their throughput is not high enough to process data from large genomes. The thesis describes the first FPGA-based error-correction tool, which is designed to improve the throughput of DNA error correction for Illumina reads. The base algorithm of the FPGA implementation is BLESS which is highly accurate but slow. The hardware implemented on the FPGA consists of a Bloom filter that is the main data structure of BLESS and the error-correction subroutines in BLESS. The design is compared with the software version of BLESS, and two other leading tools. The results show significant improvements in speed for the FPGA-based implementation with comparable accuracy of error correction.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2017-02-28 without embargo terms","The student, Anand Ramachandran, accepted the attached license on 2016-12-05 at 10:00.","The student, Anand Ramachandran, submitted this Thesis for approval on 2016-12-05 at 10:11.","This Thesis was approved for publication on 2016-12-05 at 16:44.","DSpace SAF Submission Ingestion Package generated from Vireo submission #10429 on 2017-02-28 at 14:55:18","Made available in DSpace on 2017-03-01T15:49:26Z (GMT). No. of bitstreams: 2 RAMACHANDRAN-THESIS-2016.pdf: 660590 bytes, checksum: 86046a62d760f1bfab24d178a81790be (MD5) LICENSE.txt: 4215 bytes, checksum: 497bc08f6b872ff7771f5df624a337b5 (MD5) Previous issue date: 2016-12-05"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["FPGA acceleration of DNA error correction"]}]}],"canonical_facts":{"dc:contributor":["Chen, Deming"],"dc:creator":["Ramachandran, Anand"],"dc:date":["2017-03-01T15:49:26Z","2016-12-05","2016-12"],"dc:description":["Correcting errors in DNA sequencing data is an important process that can improve the quality of downstream analyses using the data. Even though many error-correction methods have been proposed for Illumina reads, their throughput is not high enough to process data from large genomes. The thesis describes the first FPGA-based error-correction tool, which is designed to improve the throughput of DNA error correction for Illumina reads. The base algorithm of the FPGA implementation is BLESS which is highly accurate but slow. The hardware implemented on the FPGA consists of a Bloom filter that is the main data structure of BLESS and the error-correction subroutines in BLESS. The design is compared with the software version of BLESS, and two other leading tools. The results show significant improvements in speed for the FPGA-based implementation with comparable accuracy of error correction.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2017-02-28 without embargo terms","The student, Anand Ramachandran, accepted the attached license on 2016-12-05 at 10:00.","The student, Anand Ramachandran, submitted this Thesis for approval on 2016-12-05 at 10:11.","This Thesis was approved for publication on 2016-12-05 at 16:44.","DSpace SAF Submission Ingestion Package generated from Vireo submission #10429 on 2017-02-28 at 14:55:18","Made available in DSpace on 2017-03-01T15:49:26Z (GMT). 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