{"id":"https://openalex.org/W3043360048","doi":"https://doi.org/10.1109/rivf48685.2020.9140768","title":"Heterogeneous Hardware-assisted Parallel Processing for BWA-MEM DNA Alignment","display_name":"Heterogeneous Hardware-assisted Parallel Processing for BWA-MEM DNA Alignment","publication_year":2020,"publication_date":"2020-07-15","ids":{"openalex":"https://openalex.org/W3043360048","doi":"https://doi.org/10.1109/rivf48685.2020.9140768","mag":"3043360048"},"language":"en","primary_location":{"id":"doi:10.1109/rivf48685.2020.9140768","is_oa":false,"landing_page_url":"https://doi.org/10.1109/rivf48685.2020.9140768","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 RIVF International Conference on Computing and Communication Technologies (RIVF)","raw_type":"proceedings-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/A5052625146","display_name":"Binh Kieu-Do-Nguyen","orcid":"https://orcid.org/0000-0001-7240-7203"},"institutions":[{"id":"https://openalex.org/I123565023","display_name":"Vietnam National University Ho Chi Minh City","ror":"https://ror.org/00waaqh38","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023"]},{"id":"https://openalex.org/I47265099","display_name":"Ho Chi Minh City University of Technology","ror":"https://ror.org/04qva2324","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I47265099"]}],"countries":["VN"],"is_corresponding":true,"raw_author_name":"Binh Kieu-Do-Nguyen","raw_affiliation_strings":["HCMC Univerisity of Technology VNU-HCM, Vietnam"],"affiliations":[{"raw_affiliation_string":"HCMC Univerisity of Technology VNU-HCM, Vietnam","institution_ids":["https://openalex.org/I47265099","https://openalex.org/I123565023"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074161542","display_name":"Cuong Pham\u2010Quoc","orcid":"https://orcid.org/0000-0003-2917-1244"},"institutions":[{"id":"https://openalex.org/I20529979","display_name":"University of Electro-Communications","ror":"https://ror.org/02x73b849","country_code":"JP","type":"education","lineage":["https://openalex.org/I20529979"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Cuong Pham-Quoc","raw_affiliation_strings":["The University of Electro-Communication, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"The University of Electro-Communication, Tokyo, Japan","institution_ids":["https://openalex.org/I20529979"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042912660","display_name":"Cong\u2010Kha Pham","orcid":"https://orcid.org/0000-0001-5255-4919"},"institutions":[{"id":"https://openalex.org/I20529979","display_name":"University of Electro-Communications","ror":"https://ror.org/02x73b849","country_code":"JP","type":"education","lineage":["https://openalex.org/I20529979"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Cong-Kha Pham","raw_affiliation_strings":["The University of Electro-Communication, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"The University of Electro-Communication, Tokyo, Japan","institution_ids":["https://openalex.org/I20529979"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5052625146"],"corresponding_institution_ids":["https://openalex.org/I123565023","https://openalex.org/I47265099"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.0659879,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"1303","issue":null,"first_page":"1","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.989799976348877,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9811000227928162,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8133653402328491},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7172734141349792},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.5229461789131165},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.5155260562896729},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5011842250823975},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.4369509816169739},{"id":"https://openalex.org/keywords/parallel-processing","display_name":"Parallel processing","score":0.41998475790023804},{"id":"https://openalex.org/keywords/computer-engineering","display_name":"Computer engineering","score":0.3751699924468994}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8133653402328491},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7172734141349792},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.5229461789131165},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.5155260562896729},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5011842250823975},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.4369509816169739},{"id":"https://openalex.org/C106515295","wikidata":"https://www.wikidata.org/wiki/Q26806595","display_name":"Parallel processing","level":2,"score":0.41998475790023804},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.3751699924468994},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/rivf48685.2020.9140768","is_oa":false,"landing_page_url":"https://doi.org/10.1109/rivf48685.2020.9140768","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 RIVF International Conference on Computing and Communication Technologies (RIVF)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.49000000953674316}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1573552135","https://openalex.org/W1995448823","https://openalex.org/W2014707208","https://openalex.org/W2052601433","https://openalex.org/W2087064593","https://openalex.org/W2095680943","https://openalex.org/W2097341408","https://openalex.org/W2103441770","https://openalex.org/W2112113834","https://openalex.org/W2124985265","https://openalex.org/W2150473419","https://openalex.org/W2218392081","https://openalex.org/W2908267306","https://openalex.org/W2944735424","https://openalex.org/W4235611153","https://openalex.org/W4241026011","https://openalex.org/W4394666350","https://openalex.org/W6674561012"],"related_works":["https://openalex.org/W3037187668","https://openalex.org/W4234772502","https://openalex.org/W2380685755","https://openalex.org/W2252100032","https://openalex.org/W2963436428","https://openalex.org/W4400978025","https://openalex.org/W2734796617","https://openalex.org/W2017449983","https://openalex.org/W2340724640","https://openalex.org/W1970073092"],"abstract_inverted_index":{"With":[0],"the":[1,6,34,42,79,92,115,140],"fast":[2],"development":[3],"in":[4,46,108,120],"technology,":[5],"amount":[7],"of":[8,29,41,65,75,114],"genetic":[9],"data":[10,126],"needs":[11],"to":[12,72,135],"be":[13],"processed":[14],"grows":[15],"exponentially.":[16],"As":[17],"an":[18,96],"evidence":[19],"for":[20,77],"this":[21,66,88,109],"fact,":[22],"there":[23,56],"have":[24],"been":[25],"a":[26,73],"huge":[27],"number":[28,74],"modern":[30],"tools/approaches":[31],"published":[32],"over":[33],"last":[35],"decades.":[36],"DNA":[37,98],"alignment":[38,99],"is":[39],"one":[40],"most":[43],"important":[44],"stages":[45],"biological":[47],"investigations,":[48],"and":[49,118],"it":[50,68],"also":[51],"attracts":[52],"much":[53],"attention.":[54],"Although":[55],"exists":[57],"many":[58],"algorithms":[59],"that":[60],"significantly":[61],"improve":[62],"processing":[63],"time":[64],"stage,":[67],"still":[69],"takes":[70],"up":[71,134],"days":[76],"aligning":[78],"whole":[80],"human":[81],"genome":[82],"even":[83],"with":[84,101,139],"large":[85],"clusters.":[86],"In":[87],"work,":[89],"we":[90],"accelerate":[91],"improved":[93],"BWA-MEM":[94],"algorithm,":[95,100],"efficient":[97],"our":[102],"proposed":[103],"architecture.":[104],"The":[105],"implementation":[106],"discussed":[107],"work":[110],"focuses":[111],"on":[112],"exploitation":[113],"pipeline":[116],"architecture":[117],"optimization":[119],"memory":[121],"access":[122],"as":[123,125],"well":[124],"communication.":[127],"Our":[128],"system":[129],"can":[130],"obtain":[131],"speed-ups":[132],"by":[133],"14.3\u00d7":[136],"when":[137],"compared":[138],"other":[141],"computing":[142],"platforms.":[143]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
