{"id":"https://openalex.org/W2573785130","doi":"https://doi.org/10.1145/3039902.3039910","title":"An Efficient GPUAccelerated Implementation of Genomic Short Read Mapping with BWAMEM","display_name":"An Efficient GPUAccelerated Implementation of Genomic Short Read Mapping with BWAMEM","publication_year":2017,"publication_date":"2017-01-11","ids":{"openalex":"https://openalex.org/W2573785130","doi":"https://doi.org/10.1145/3039902.3039910","mag":"2573785130"},"language":"en","primary_location":{"id":"doi:10.1145/3039902.3039910","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3039902.3039910","pdf_url":null,"source":{"id":"https://openalex.org/S4210193905","display_name":"ACM SIGARCH Computer Architecture News","issn_l":"0163-5964","issn":["0163-5964","1943-5851"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320740","host_organization_name":"ACM SIGARCH","host_organization_lineage":["https://openalex.org/P4310320740"],"host_organization_lineage_names":["ACM SIGARCH"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM SIGARCH Computer Architecture News","raw_type":"journal-article"},"type":"article","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/A5083450136","display_name":"Ernst Houtgast","orcid":null},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Ernst Joachim Houtgast","raw_affiliation_strings":["Computer Engineering Lab, TU Delft, Delft, The Netherlands and Bluebee, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Computer Engineering Lab, TU Delft, Delft, The Netherlands and Bluebee, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071212678","display_name":"Vlad-Mihai Sima","orcid":"https://orcid.org/0000-0002-5333-7892"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"VladMihai Sima","raw_affiliation_strings":["Bluebee, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Bluebee, The Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058128591","display_name":"Koen Bertels","orcid":"https://orcid.org/0000-0001-9310-4885"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Koen Bertels","raw_affiliation_strings":["Computer Engineering Lab, TU Delft, Delft, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Computer Engineering Lab, TU Delft, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021955713","display_name":"Zaid Al-Ars","orcid":"https://orcid.org/0000-0001-7670-8572"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Zaid AlArs","raw_affiliation_strings":["Computer Engineering Lab, TU Delft, Delft, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Computer Engineering Lab, TU Delft, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5083450136"],"corresponding_institution_ids":["https://openalex.org/I98358874"],"apc_list":null,"apc_paid":null,"fwci":0.7573,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.6922636,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"44","issue":"4","first_page":"38","last_page":"43"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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":0.9987000226974487,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9872999787330627,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.9395886659622192},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7717604637145996},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6767889261245728},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5350647568702698},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.4983384609222412},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.44976526498794556},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3373124599456787},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33570319414138794},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.32965996861457825},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32812437415122986},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.29706594347953796},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.17201191186904907},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.14912214875221252}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.9395886659622192},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7717604637145996},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6767889261245728},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5350647568702698},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.4983384609222412},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.44976526498794556},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3373124599456787},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33570319414138794},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.32965996861457825},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32812437415122986},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.29706594347953796},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.17201191186904907},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.14912214875221252},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3039902.3039910","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3039902.3039910","pdf_url":null,"source":{"id":"https://openalex.org/S4210193905","display_name":"ACM SIGARCH Computer Architecture News","issn_l":"0163-5964","issn":["0163-5964","1943-5851"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320740","host_organization_name":"ACM SIGARCH","host_organization_lineage":["https://openalex.org/P4310320740"],"host_organization_lineage_names":["ACM SIGARCH"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM SIGARCH Computer Architecture News","raw_type":"journal-article"},{"id":"pmh:oai:tudelft.nl:uuid:078c3e89-a22b-41ae-8e5c-1f63cc640518","is_oa":false,"landing_page_url":"http://resolver.tudelft.nl/uuid:078c3e89-a22b-41ae-8e5c-1f63cc640518","pdf_url":null,"source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.5299999713897705,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1995448823","https://openalex.org/W2033173420","https://openalex.org/W2065461987","https://openalex.org/W2087064593","https://openalex.org/W2095680943","https://openalex.org/W2104846587","https://openalex.org/W2107824361","https://openalex.org/W2117683095","https://openalex.org/W2165949232","https://openalex.org/W2218392081","https://openalex.org/W2466053952","https://openalex.org/W2517387426","https://openalex.org/W2620558550","https://openalex.org/W6672364634"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W98480971","https://openalex.org/W1980160788","https://openalex.org/W1656096860","https://openalex.org/W2095928260","https://openalex.org/W2268149564","https://openalex.org/W1984739956","https://openalex.org/W2763312740","https://openalex.org/W2043140447"],"abstract_inverted_index":{"Next":[0],"Generation":[1],"Sequencing":[2],"techniques":[3],"have":[4],"resulted":[5],"in":[6,10,188],"an":[7,131],"exponential":[8],"growth":[9],"the":[11,16,66,83,87,104,121,138,155,175],"generation":[12],"of":[13,18,48,60,78,94,103,114,134,179],"genetics":[14],"data,":[15],"amount":[17],"which":[19,64,153],"will":[20],"soon":[21],"rival,":[22],"if":[23],"not":[24],"overtake,":[25],"other":[26],"Big":[27],"Data":[28],"fields,":[29],"such":[30,61],"as":[31],"astronomy":[32],"and":[33],"streaming":[34],"video":[35],"services.":[36],"To":[37],"become":[38],"useful,":[39],"this":[40,135,161],"data":[41],"requires":[42,111],"processing":[43,116],"by":[44],"a":[45,70,75,91,147,177],"complex":[46],"pipeline":[47],"algorithms,":[49],"taking":[50],"multiple":[51],"days":[52],"even":[53],"on":[54,174],"large":[55],"clusters.":[56],"The":[57,98,140],"mapping":[58,88,133],"stage":[59],"genomics":[62],"pipelines,":[63],"maps":[65],"short":[67],"reads":[68],"onto":[69,120,137],"reference":[71],"genome,":[72],"takes":[73],"up":[74,168],"significant":[76],"portion":[77],"execution":[79],"time.":[80],"BWA-MEM":[81,95,107],"is":[82,96,118,128,154,163],"de-facto":[84],"industry-standard":[85],"for":[86,130,165,193],"stage.":[89],"Here,":[90],"GPU-accelerated":[92],"implementation":[93,145],"proposed.":[97],"Seed":[99],"Extension":[100],"phase,":[101],"one":[102],"three":[105],"main":[106],"algorithm":[108],"phases":[109],"that":[110],"between":[112],"30%-50%":[113],"overall":[115,150],"time,":[117],"offloaded":[119],"GPU.":[122,139],"A":[123],"thorough":[124],"design":[125],"space":[126],"analysis":[127],"presented":[129],"optimized":[132],"phase":[136],"re-":[141],"sulting":[142],"systolic-array":[143],"based":[144],"obtains":[146],"two-":[148],"fold":[149],"application-level":[151],"speedup,":[152],"maximum":[156],"theoretically":[157],"achievable":[158],"speedup.":[159],"Moreover,":[160],"speedup":[162],"sustained":[164],"systems":[166],"with":[167],"to":[169,183],"twenty-two":[170],"logical":[171],"cores.":[172],"Based":[173],"findings,":[176],"number":[178],"suggestions":[180],"are":[181],"made":[182],"improve":[184],"GPU":[185],"architecture,":[186],"resulting":[187],"potentially":[189],"greatly":[190],"increased":[191],"performance":[192],"bioinformatics-class":[194],"algorithms.":[195]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":5},{"year":2016,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}