{"id":"https://openalex.org/W4362602312","doi":"https://doi.org/10.1109/tcbb.2023.3264514","title":"Porting and Optimizing BWA-MEM2 Using the Fujitsu A64FX Processor","display_name":"Porting and Optimizing BWA-MEM2 Using the Fujitsu A64FX Processor","publication_year":2023,"publication_date":"2023-04-05","ids":{"openalex":"https://openalex.org/W4362602312","doi":"https://doi.org/10.1109/tcbb.2023.3264514","pmid":"https://pubmed.ncbi.nlm.nih.gov/37018085"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3264514","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://upcommons.upc.edu/bitstream/2117/386457/1/Langarita%20et%20al.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072178927","display_name":"Rub\u00e9n Langarita","orcid":"https://orcid.org/0000-0002-6080-724X"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Rub\u00e9n Langarita","raw_affiliation_strings":["Barcelona Supercomputing Center, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049697257","display_name":"Adri\u00e0 Armejach","orcid":"https://orcid.org/0000-0003-2869-668X"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Adri\u00e0 Armejach","raw_affiliation_strings":["Barcelona Supercomputing Center, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028406181","display_name":"Pablo Ib\u00e1\u00f1ez","orcid":"https://orcid.org/0000-0002-5916-7898"},"institutions":[{"id":"https://openalex.org/I255234318","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28","country_code":"ES","type":"education","lineage":["https://openalex.org/I255234318"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Pablo Ib\u00e1\u00f1ez","raw_affiliation_strings":["Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, Zaragoza, Spain"],"affiliations":[{"raw_affiliation_string":"Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, Zaragoza, Spain","institution_ids":["https://openalex.org/I255234318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073821260","display_name":"Jes\u00fas Alastruey-Bened\u00e9","orcid":"https://orcid.org/0000-0003-4164-5078"},"institutions":[{"id":"https://openalex.org/I255234318","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28","country_code":"ES","type":"education","lineage":["https://openalex.org/I255234318"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jes\u00fas Alastruey-Bened\u00e9","raw_affiliation_strings":["Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, Zaragoza, Spain"],"affiliations":[{"raw_affiliation_string":"Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, Zaragoza, Spain","institution_ids":["https://openalex.org/I255234318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088729105","display_name":"Miquel Moret\u00f3","orcid":"https://orcid.org/0000-0002-9848-8758"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Miquel Moret\u00f3","raw_affiliation_strings":["Barcelona Supercomputing Center, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.17,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":5,"citation_normalized_percentile":{"value":0.743383,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":92},"biblio":{"volume":"20","issue":"5","first_page":"3139","last_page":"3153"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T11992","display_name":"CCD and CMOS Imaging Sensors","score":0.9889,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11992","display_name":"CCD and CMOS Imaging Sensors","score":0.9889,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11044","display_name":"Particle Detector Development and Performance","score":0.9702,"subfield":{"id":"https://openalex.org/subfields/3106","display_name":"Nuclear and High Energy Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10191","display_name":"Robotics and Sensor-Based Localization","score":0.9664,"subfield":{"id":"https://openalex.org/subfields/2202","display_name":"Aerospace Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.84413576}],"concepts":[{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.84413576},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.58700085},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.5232531},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.35312602},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.11399844}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3264514","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/386457","pdf_url":"https://upcommons.upc.edu/bitstream/2117/386457/1/Langarita%20et%20al.pdf","source":{"id":"https://openalex.org/S4306400551","display_name":"UPCommons (Polytechnic University of Catalonia)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":["Universitat Polit\u00e8cnica de Catalunya"],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"http://zaguan.unizar.es/record/125986","pdf_url":"https://zaguan.unizar.es/record/125986/files/texto_completo.pdf","source":{"id":"https://openalex.org/S4306402461","display_name":"Zaguan (Universidad de Zaragoza)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37018085","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/386457","pdf_url":"https://upcommons.upc.edu/bitstream/2117/386457/1/Langarita%20et%20al.pdf","source":{"id":"https://openalex.org/S4306400551","display_name":"UPCommons (Polytechnic University of Catalonia)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":["Universitat Polit\u00e8cnica de Catalunya"],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.77,"display_name":"Affordable and clean energy"}],"grants":[],"datasets":[],"versions":[],"referenced_works_count":42,"referenced_works":["https://openalex.org/W1828154403","https://openalex.org/W2001496424","https://openalex.org/W2016219933","https://openalex.org/W2025648894","https://openalex.org/W2068448872","https://openalex.org/W2093931624","https://openalex.org/W2100751585","https://openalex.org/W2103441770","https://openalex.org/W2104846587","https://openalex.org/W2105321788","https://openalex.org/W2124985265","https://openalex.org/W2128793361","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2135326109","https://openalex.org/W2146379626","https://openalex.org/W2146496959","https://openalex.org/W2524329555","https://openalex.org/W2555913832","https://openalex.org/W2560228154","https://openalex.org/W2766525247","https://openalex.org/W2788876413","https://openalex.org/W2789843538","https://openalex.org/W2896415993","https://openalex.org/W2904665340","https://openalex.org/W2923143097","https://openalex.org/W2939705846","https://openalex.org/W2950629094","https://openalex.org/W2971559821","https://openalex.org/W3021908862","https://openalex.org/W3033334618","https://openalex.org/W3086678357","https://openalex.org/W3097283637","https://openalex.org/W3105003914","https://openalex.org/W3123542955","https://openalex.org/W3165246342","https://openalex.org/W4214546858","https://openalex.org/W4236236547","https://openalex.org/W4247053599","https://openalex.org/W4254502766","https://openalex.org/W4281647104","https://openalex.org/W4361017256"],"related_works":["https://openalex.org/W2907301531","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2392011550","https://openalex.org/W2389790172","https://openalex.org/W2368028869","https://openalex.org/W2356921469","https://openalex.org/W2187911614","https://openalex.org/W2186516977","https://openalex.org/W1583729815"],"abstract_inverted_index":{"Sequence":[0],"alignment":[1],"pipelines":[2],"for":[3,170],"human":[4],"genomes":[5],"are":[6],"an":[7,54],"emerging":[8],"workload":[9],"that":[10,114,146,154],"will":[11],"dominate":[12],"in":[13,24,59,62,139],"the":[14,25,40,44,50,88,103,111,116,140,148,156,167],"precision":[15],"medicine":[16],"field.":[17],"BWA-MEM2":[18,38,72,127],"is":[19,151,173],"a":[20,132],"tool":[21],"widely":[22],"used":[23,169],"scientific":[26],"community":[27],"to":[28,39,105,122,136],"perform":[29],"read":[30],"mapping":[31],"studies.":[32],"In":[33],"this":[34,84,171],"paper,":[35],"we":[36,48,86,98,128],"port":[37],"AArch64":[41],"architecture":[42],"using":[43,76],"ARMv8-A":[45],"specification,":[46],"and":[47,61,130],"compare":[49],"resulting":[51],"version":[52],"against":[53],"Intel":[55],"Skylake":[56,157],"system":[57],"both":[58],"performance":[60,138,150],"energy-to-solution.":[63],"The":[64,108],"porting":[65,126],"effort":[66],"entails":[67],"numerous":[68],"code":[69,85,168],"modifications,":[70],"since":[71],"implements":[73],"certain":[74],"kernels":[75],"x86_64":[77],"specific":[78],"intrinsics,":[79],"e.g.,":[80],"AVX-512.":[81],"To":[82],"adapt":[83],"use":[87,99],"recently":[89],"introduced":[90],"Arm's":[91],"Scalable":[92],"Vector":[93],"Extensions":[94],"(SVE).":[95],"More":[96],"specifically,":[97],"Fujitsu's":[100],"A64FX":[101,109,141,149,159],"processor,":[102],"first":[104],"implement":[106,131],"SVE.":[107],"powers":[110],"Fugaku":[112],"Supercomputer":[113],"led":[115],"Top500":[117],"ranking":[118],"from":[119],"June":[120],"2020":[121],"November":[123],"2021.":[124],"After":[125],"define":[129],"number":[133],"of":[134,155],"optimizations":[135],"improve":[137],"target":[142],"architecture.":[143],"We":[144],"show":[145],"while":[147],"lower":[152],"than":[153],"system,":[158],"delivers":[160],"11.6%":[161],"better":[162],"energy-to-solution":[163],"on":[164],"average.":[165],"All":[166],"article":[172],"available":[174],"at":[175],"https://gitlab.bsc.es/rlangari/bwa-a64fx":[178],".":[179]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W4362602312","counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2025-01-19T01:40:18.852097","created_date":"2023-04-06"}