{"id":"https://openalex.org/W2125109709","doi":"https://doi.org/10.1109/ipdps.2009.5160924","title":"Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA","display_name":"Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA","publication_year":2009,"publication_date":"2009-05-01","ids":{"openalex":"https://openalex.org/W2125109709","doi":"https://doi.org/10.1109/ipdps.2009.5160924","mag":"2125109709"},"language":"en","primary_location":{"id":"doi:10.1109/ipdps.2009.5160924","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2009.5160924","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 IEEE International Symposium on Parallel &amp; Distributed Processing","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081591983","display_name":"Haixiang Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Haixiang Shi","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore","School of Computer Engineering, Nanyang Technological University, Singapore, 639798"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore, 639798","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"B. Schmidt","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore","School of Computer Engineering, Nanyang Technological University, Singapore, 639798"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore, 639798","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100620772","display_name":"Weiguo Liu","orcid":"https://orcid.org/0000-0001-8834-0453"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Weiguo Liu","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore","School of Computer Engineering, Nanyang Technological University, Singapore, 639798"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore, 639798","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014404405","display_name":"Wolfgang M\u00fcller\u2010Wittig","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"W. Muller-Wittig","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore","School of Computer Engineering, Nanyang Technological University, Singapore, 639798"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore, 639798","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9958000183105469,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9761000275611877,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8004353046417236},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.7229149341583252},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6920040845870972},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.636561393737793},{"id":"https://openalex.org/keywords/sanger-sequencing","display_name":"Sanger sequencing","score":0.6079072952270508},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5848091840744019},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5707587003707886},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.49363839626312256},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.4913979768753052},{"id":"https://openalex.org/keywords/massive-parallel-sequencing","display_name":"Massive parallel sequencing","score":0.4451601505279541},{"id":"https://openalex.org/keywords/error-detection-and-correction","display_name":"Error detection and correction","score":0.440624862909317},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.4155590534210205},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.30019277334213257},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2671777009963989},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.17563015222549438},{"id":"https://openalex.org/keywords/wireless","display_name":"Wireless","score":0.11708837747573853},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11329427361488342},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09468618035316467},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.07596585154533386}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8004353046417236},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.7229149341583252},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6920040845870972},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.636561393737793},{"id":"https://openalex.org/C76818968","wikidata":"https://www.wikidata.org/wiki/Q181940","display_name":"Sanger sequencing","level":4,"score":0.6079072952270508},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5848091840744019},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5707587003707886},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.49363839626312256},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.4913979768753052},{"id":"https://openalex.org/C192800701","wikidata":"https://www.wikidata.org/wiki/Q6784807","display_name":"Massive parallel sequencing","level":4,"score":0.4451601505279541},{"id":"https://openalex.org/C103088060","wikidata":"https://www.wikidata.org/wiki/Q1062839","display_name":"Error detection and correction","level":2,"score":0.440624862909317},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.4155590534210205},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.30019277334213257},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2671777009963989},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.17563015222549438},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.11708837747573853},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11329427361488342},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09468618035316467},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.07596585154533386},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/ipdps.2009.5160924","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2009.5160924","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 IEEE International Symposium on Parallel &amp; Distributed Processing","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.157.1952","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.157.1952","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.hicomb.org/papers/HICOMB2009-03.pdf","raw_type":"text"},{"id":"pmh:oai:fraunhofer.de:N-118675","is_oa":false,"landing_page_url":"http://publica.fraunhofer.de/documents/N-118675.html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400801","display_name":"Publikationsdatenbank der Fraunhofer-Gesellschaft (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Fraunhofer IGD","raw_type":"Conference Paper"},{"id":"pmh:oai:publica.fraunhofer.de:publica/363936","is_oa":false,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/363936","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conference paper"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5099999904632568,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320335846","display_name":"Biomedical Research Council","ror":"https://ror.org/03xy0wx88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W2000636639","https://openalex.org/W2011652244","https://openalex.org/W2023911006","https://openalex.org/W2028499920","https://openalex.org/W2048772283","https://openalex.org/W2072193858","https://openalex.org/W2123845384","https://openalex.org/W2127651281","https://openalex.org/W2131088968","https://openalex.org/W2135196291","https://openalex.org/W2136651963","https://openalex.org/W2138270253","https://openalex.org/W2144662851","https://openalex.org/W2151017710","https://openalex.org/W2155503253","https://openalex.org/W2155845142","https://openalex.org/W2164631357","https://openalex.org/W2166621589","https://openalex.org/W2171475724","https://openalex.org/W2616754551","https://openalex.org/W3138798301"],"related_works":["https://openalex.org/W2274887458","https://openalex.org/W2922341075","https://openalex.org/W367034151","https://openalex.org/W4379373911","https://openalex.org/W2024116089","https://openalex.org/W2323445759","https://openalex.org/W1911510163","https://openalex.org/W4255788549","https://openalex.org/W2921468924","https://openalex.org/W2778510927"],"abstract_inverted_index":{"Emerging":[0],"DNA":[1,42],"sequencing":[2,11,35,78],"technologies":[3],"open":[4],"up":[5],"exciting":[6],"new":[7],"opportunities":[8],"for":[9,40,76],"genome":[10],"by":[12],"generating":[13],"read":[14],"data":[15,65],"with":[16,53,61],"a":[17,72,100],"massive":[18],"throughput.":[19],"However,":[20],"produced":[21],"reads":[22],"are":[23],"significantly":[24],"shorter":[25],"and":[26,57,90,109],"more":[27],"error-prone":[28,55],"compared":[29],"to":[30],"the":[31,92],"traditional":[32],"Sanger":[33],"shotgun":[34],"method.":[36],"This":[37],"poses":[38],"challenges":[39],"de-novo":[41],"fragment":[43],"assembly":[44],"algorithms":[45],"in":[46,80],"terms":[47],"of":[48],"both":[49],"accuracy":[50],"(to":[51,59],"deal":[52,60],"short,":[54],"reads)":[56],"scalability":[58],"very":[62],"large":[63],"input":[64],"sets).":[66],"In":[67],"this":[68],"paper":[69],"we":[70],"present":[71],"scalable":[73],"parallel":[74],"algorithm":[75],"correcting":[77],"errors":[79],"high-throughput":[81],"short-read":[82],"data.":[83],"It":[84],"is":[85],"based":[86],"on":[87,99],"spectral":[88],"alignment":[89],"uses":[91],"CUDA":[93],"programming":[94],"model.":[95],"Our":[96],"computational":[97],"experiments":[98],"GTX":[101],"280":[102],"GPU":[103],"show":[104],"runtime":[105],"savings":[106],"between":[107],"10":[108],"19":[110],"times":[111],"(for":[112],"different":[113],"error-rates":[114],"using":[115],"simulated":[116],"datasets":[117],"as":[118,120],"well":[119],"real":[121],"Solexa/Illumina":[122],"datasets).":[123]},"counts_by_year":[{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
