{"id":"https://openalex.org/W4388801332","doi":"https://doi.org/10.1093/bioinformatics/btad701","title":"WFA-GPU: gap-affine pairwise read-alignment using GPUs","display_name":"WFA-GPU: gap-affine pairwise read-alignment using GPUs","publication_year":2023,"publication_date":"2023-11-16","ids":{"openalex":"https://openalex.org/W4388801332","doi":"https://doi.org/10.1093/bioinformatics/btad701","pmid":"https://pubmed.ncbi.nlm.nih.gov/37975878"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad701","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad701/53483097/btad701.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad701/53483097/btad701.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005302308","display_name":"Quim Aguado-Puig","orcid":"https://orcid.org/0000-0003-4871-3192"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Quim Aguado-Puig","raw_affiliation_strings":["Departament d\u2019Arquitectura de Computadors i Sistemes Operatius, Universitat Aut\u00f2noma de Barcelona , Barcelona 08193, Spain"],"raw_orcid":"https://orcid.org/0000-0003-4871-3192","affiliations":[{"raw_affiliation_string":"Departament d\u2019Arquitectura de Computadors i Sistemes Operatius, Universitat Aut\u00f2noma de Barcelona , Barcelona 08193, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029739066","display_name":"Max Doblas","orcid":"https://orcid.org/0000-0002-8909-3033"},"institutions":[{"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"]},{"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"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Max Doblas","raw_affiliation_strings":["Computer Sciences Department, Barcelona Supercomputing Center , Barcelona 08034, Spain","Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Sciences Department, Barcelona Supercomputing Center , Barcelona 08034, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013788676","display_name":"Christos Matzoros","orcid":null},"institutions":[{"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"]},{"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"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Christos Matzoros","raw_affiliation_strings":["Computer Sciences Department, Barcelona Supercomputing Center , Barcelona 08034, Spain","Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Sciences Department, Barcelona Supercomputing Center , Barcelona 08034, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031177539","display_name":"Antonio Espinosa","orcid":"https://orcid.org/0000-0002-6460-3789"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Antonio Espinosa","raw_affiliation_strings":["Departament d\u2019Arquitectura de Computadors i Sistemes Operatius, Universitat Aut\u00f2noma de Barcelona , Barcelona 08193, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departament d\u2019Arquitectura de Computadors i Sistemes Operatius, Universitat Aut\u00f2noma de Barcelona , Barcelona 08193, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051140834","display_name":"Juan Carlos Moure","orcid":"https://orcid.org/0000-0001-6697-0331"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Juan Carlos Moure","raw_affiliation_strings":["Departament d\u2019Arquitectura de Computadors i Sistemes Operatius, Universitat Aut\u00f2noma de Barcelona , Barcelona 08193, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departament d\u2019Arquitectura de Computadors i Sistemes Operatius, Universitat Aut\u00f2noma de Barcelona , Barcelona 08193, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052502603","display_name":"Santiago Marco\u2010Sola","orcid":"https://orcid.org/0000-0001-7951-3914"},"institutions":[{"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"]},{"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"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Santiago Marco-Sola","raw_affiliation_strings":["Computer Sciences Department, Barcelona Supercomputing Center , Barcelona 08034, Spain","Departament d\u2019Arquitectura de Computadors, Universitat Polit\u00e8cnica de Catalunya , Barcelona 08034, Spain","Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain"],"raw_orcid":"https://orcid.org/0000-0001-7951-3914","affiliations":[{"raw_affiliation_string":"Computer Sciences Department, Barcelona Supercomputing Center , Barcelona 08034, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Departament d\u2019Arquitectura de Computadors, Universitat Polit\u00e8cnica de Catalunya , Barcelona 08034, Spain","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"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/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"]},{"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"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Miquel Moreto","raw_affiliation_strings":["Computer Sciences Department, Barcelona Supercomputing Center , Barcelona 08034, Spain","Departament d\u2019Arquitectura de Computadors, Universitat Polit\u00e8cnica de Catalunya , Barcelona 08034, Spain","Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Sciences Department, Barcelona Supercomputing Center , Barcelona 08034, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Departament d\u2019Arquitectura de Computadors, Universitat Polit\u00e8cnica de Catalunya , Barcelona 08034, Spain","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5005302308"],"corresponding_institution_ids":["https://openalex.org/I123044942"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.0703,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.94453647,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"39","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9258000254631042,"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":0.9258000254631042,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.01140000019222498,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.008700000122189522,"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":0.872238039970398},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6609958410263062},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6087266802787781},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.5968512892723083},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.5823080539703369},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.5140279531478882},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.46496349573135376},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.4102887213230133},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.3541344106197357},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.34366732835769653},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1477195918560028},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.08729684352874756}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.872238039970398},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6609958410263062},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6087266802787781},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.5968512892723083},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.5823080539703369},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.5140279531478882},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.46496349573135376},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.4102887213230133},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.3541344106197357},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.34366732835769653},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1477195918560028},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.08729684352874756},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btad701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad701","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad701/53483097/btad701.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37975878","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37975878","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":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:upcommons.upc.edu:2117/397356","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/397356","pdf_url":"https://upcommons.upc.edu/bitstreams/e6e7f3a8-c647-4567-ac93-f87d3c6d9d06/download","source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"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":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:ddd.uab.cat:306037","is_oa":true,"landing_page_url":"https://ddd.uab.cat/record/306037","pdf_url":"https://ddd.uab.cat/pub/artpub/2023/306037/2023-WFA-GPU-bioinformatics.pdf","source":{"id":"https://openalex.org/S4306400380","display_name":"Dip\u00f2sit Digital de Documents de la UAB (Universitat Aut\u00f2noma de Barcelona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123044942","host_organization_name":"Universitat Aut\u00f2noma de Barcelona","host_organization_lineage":["https://openalex.org/I123044942"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10697739","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10697739","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10697739/pdf/btad701.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad701","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad701/53483097/btad701.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1622782223","display_name":null,"funder_award_id":"MCIN/AEI/10","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1643949827","display_name":null,"funder_award_id":"AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G2064873908","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G2262748287","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G2601397997","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2855141111","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320326262","funder_display_name":"Ministerio de Asuntos Econ\u00f3micos y Transformaci\u00f3n Digital, Gobierno de Espa\u00f1a"},{"id":"https://openalex.org/G3005324705","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G300979063","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3219925899","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3222096693","display_name":null,"funder_award_id":"TIN2015-65316-P","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3418367361","display_name":null,"funder_award_id":"RYC-2016-21104","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3480869486","display_name":null,"funder_award_id":"13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3653114660","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320326262","funder_display_name":"Ministerio de Asuntos Econ\u00f3micos y Transformaci\u00f3n Digital, Gobierno de Espa\u00f1a"},{"id":"https://openalex.org/G3681454997","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G386121643","display_name":null,"funder_award_id":"TIN2015-65316-P","funder_id":"https://openalex.org/F4320326262","funder_display_name":"Ministerio de Asuntos Econ\u00f3micos y Transformaci\u00f3n Digital, Gobierno de Espa\u00f1a"},{"id":"https://openalex.org/G4042783231","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4045093968","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G410571670","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G4107300439","display_name":null,"funder_award_id":"001-P-001723","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G4337097655","display_name":null,"funder_award_id":"2021-SGR-00574","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G451917667","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G4619247980","display_name":null,"funder_award_id":"RYC-2016-21104","funder_id":"https://openalex.org/F4320326262","funder_display_name":"Ministerio de Asuntos Econ\u00f3micos y Transformaci\u00f3n Digital, Gobierno de Espa\u00f1a"},{"id":"https://openalex.org/G4715039861","display_name":null,"funder_award_id":"2017-SGR-313","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G4882408770","display_name":null,"funder_award_id":"AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320326262","funder_display_name":"Ministerio de Asuntos Econ\u00f3micos y Transformaci\u00f3n Digital, Gobierno de Espa\u00f1a"},{"id":"https://openalex.org/G4976336944","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G4986017096","display_name":null,"funder_award_id":"001-P-001723","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G5080475149","display_name":null,"funder_award_id":"10.13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G5539308778","display_name":null,"funder_award_id":"AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G5634946813","display_name":null,"funder_award_id":"2014-2020","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G5967599077","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G6456004180","display_name":null,"funder_award_id":"2017-SGR-1414","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G6712513641","display_name":null,"funder_award_id":"2017-SGR-1328","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G6823456974","display_name":null,"funder_award_id":"AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6870533126","display_name":null,"funder_award_id":"2014-2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7084143925","display_name":null,"funder_award_id":"AEI/10","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7096924396","display_name":null,"funder_award_id":"TIN2015-65316","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G7266728691","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7535663061","display_name":null,"funder_award_id":"AEI/10.","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G823068553","display_name":null,"funder_award_id":"IJC2020-045916-I","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G8695128545","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"},{"id":"https://openalex.org/F4320326262","display_name":"Ministerio de Asuntos Econ\u00f3micos y Transformaci\u00f3n Digital, Gobierno de Espa\u00f1a","ror":"https://ror.org/03sv46s19"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388801332.pdf"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1543636183","https://openalex.org/W1675130169","https://openalex.org/W1966822396","https://openalex.org/W1990413869","https://openalex.org/W2016219933","https://openalex.org/W2025648894","https://openalex.org/W2045821558","https://openalex.org/W2066852475","https://openalex.org/W2075996757","https://openalex.org/W2100751585","https://openalex.org/W2116699248","https://openalex.org/W2119180969","https://openalex.org/W2130200371","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2146379626","https://openalex.org/W2260037449","https://openalex.org/W2560228154","https://openalex.org/W2589905137","https://openalex.org/W2788876413","https://openalex.org/W2789843538","https://openalex.org/W2891893703","https://openalex.org/W2923143097","https://openalex.org/W2949071207","https://openalex.org/W2950354111","https://openalex.org/W2953174564","https://openalex.org/W2981145358","https://openalex.org/W2981619930","https://openalex.org/W3084730237","https://openalex.org/W3086678357","https://openalex.org/W3086684206","https://openalex.org/W4245668478","https://openalex.org/W4250981202","https://openalex.org/W6679609489","https://openalex.org/W6754904495"],"related_works":["https://openalex.org/W1963859303","https://openalex.org/W2364044215","https://openalex.org/W2389600408","https://openalex.org/W240129890","https://openalex.org/W3048701459","https://openalex.org/W2149078538","https://openalex.org/W2080146221","https://openalex.org/W2370314112","https://openalex.org/W1912958759","https://openalex.org/W2153506571"],"abstract_inverted_index":{"MOTIVATION:":[0],"Advances":[1],"in":[2],"genomics":[3],"and":[4,9,39,47,67,82,120,150,183,193,201,214,248],"sequencing":[5],"technologies":[6],"demand":[7],"faster":[8,209,221],"more":[10,61],"scalable":[11],"analysis":[12],"methods":[13,190],"that":[14,123,170],"can":[15],"process":[16],"longer":[17],"sequences":[18,41],"with":[19,160],"higher":[20],"accuracy.":[21],"However,":[22,73],"classical":[23],"pairwise":[24],"alignment":[25,54,63,137],"methods,":[26],"based":[27,110],"on":[28,90,111,191],"dynamic":[29],"programming":[30],"(DP),":[31],"impose":[32],"impractical":[33],"computational":[34],"requirements":[35],"to":[36,84,105,134,181,185,197,207,216],"align":[37],"long":[38,192,237],"noisy":[40,194],"like":[42],"those":[43],"produced":[44],"by":[45,179],"PacBio":[46],"Nanopore":[48],"technologies.":[49],"The":[50],"recently":[51],"proposed":[52],"wavefront":[53],"(WFA)":[55],"algorithm":[56],"paves":[57],"the":[58,86,112,117,126,136,174,203,229],"way":[59],"for":[60],"efficient":[62,79,162],"tools,":[64],"improving":[65],"time":[66],"memory":[68],"complexity":[69],"over":[70],"previous":[71],"methods.":[72],"high-performance":[74],"computing":[75,87],"(HPC)":[76],"platforms":[77],"require":[78],"parallel":[80,128,152],"algorithms":[81],"tools":[83,200],"exploit":[85],"resources":[88],"available":[89,252],"modern":[91,131],"accelerator-based":[92],"architectures.":[93],"RESULTS:":[94],"This":[95],"paper":[96],"presents":[97],"WFA-GPU,":[98],"a":[99,143,156,166,240],"GPU":[100,132,163,212,231],"(graphics":[101],"processing":[102],"unit)-accelerated":[103],"tool":[104],"compute":[106],"exact":[107],"gap-affine":[108],"alignments":[109],"WFA":[113,177],"algorithm.":[114],"We":[115],"present":[116],"algorithmic":[118],"adaptations":[119],"performance":[121],"optimizations":[122],"allow":[124],"exploiting":[125],"massively":[127],"capabilities":[129],"of":[130,147,219,234],"devices":[133],"accelerate":[135],"computations.":[138],"In":[139],"particular,":[140],"we":[141,168],"propose":[142],"CPU-GPU":[144],"co-design":[145],"capable":[146,233],"performing":[148],"inter-sequence":[149],"intra-sequence":[151],"sequence":[153],"alignment,":[154],"combining":[155],"succinct":[157],"WFA-data":[158],"representation":[159],"an":[161],"implementation.":[164],"As":[165],"result,":[167],"demonstrate":[169],"our":[171],"implementation":[172,178],"outperforms":[173],"original":[175],"multi-threaded":[176],"up":[180,184,206,215],"4.3\u00d7":[182],"18.2\u00d7":[186],"when":[187],"using":[188,239],"heuristic":[189],"sequences.":[195],"Compared":[196],"other":[198,211,223],"state-of-the-art":[199],"libraries,":[202],"WFA-GPU":[204,227,246],"is":[205,228],"29\u00d7":[208],"than":[210,222],"implementations":[213],"four":[217],"orders":[218],"magnitude":[220],"CPU":[224],"implementations.":[225],"Furthermore,":[226],"only":[230],"solution":[232],"correctly":[235],"aligning":[236],"reads":[238],"commodity":[241],"GPU.":[242],"AVAILABILITY":[243],"AND":[244],"IMPLEMENTATION:":[245],"code":[247],"documentation":[249],"are":[250],"publicly":[251],"at":[253],"https://github.com/quim0/WFA-GPU.":[254]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
