{"id":"https://openalex.org/W2952597168","doi":"https://doi.org/10.1093/bioinformatics/bty648","title":"Scaling read aligners to hundreds of threads on general-purpose processors","display_name":"Scaling read aligners to hundreds of threads on general-purpose processors","publication_year":2018,"publication_date":"2018-07-18","ids":{"openalex":"https://openalex.org/W2952597168","doi":"https://doi.org/10.1093/bioinformatics/bty648","mag":"2952597168","pmid":"https://pubmed.ncbi.nlm.nih.gov/30020410"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty648","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty648","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/3/421/48965413/bioinformatics_35_3_421.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/3/421/48965413/bioinformatics_35_3_421.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009556658","display_name":"Ben Langmead","orcid":"https://orcid.org/0000-0003-2437-1976"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ben Langmead","raw_affiliation_strings":["Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA","Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":"https://orcid.org/0000-0003-2437-1976","affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040039068","display_name":"Christopher Wilks","orcid":"https://orcid.org/0000-0002-9838-502X"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Wilks","raw_affiliation_strings":["Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA","Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053402647","display_name":"Valentin Antonescu","orcid":null},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Valentin Antonescu","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050517813","display_name":"Rone Charles","orcid":null},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rone Charles","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5009556658"],"corresponding_institution_ids":["https://openalex.org/I145311948"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":18.0194,"has_fulltext":true,"cited_by_count":1030,"citation_normalized_percentile":{"value":0.99643886,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"35","issue":"3","first_page":"421","last_page":"432"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5440000295639038,"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":0.5440000295639038,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.20309999585151672,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T11986","display_name":"Scientific Computing and Data Management","score":0.06509999930858612,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.898208737373352},{"id":"https://openalex.org/keywords/thread","display_name":"Thread (computing)","score":0.6894124150276184},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.6505075693130493},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6452312469482422},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5993960499763489},{"id":"https://openalex.org/keywords/xeon-phi","display_name":"Xeon Phi","score":0.5023744106292725},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.49631911516189575},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.41687777638435364}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.898208737373352},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.6894124150276184},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.6505075693130493},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6452312469482422},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5993960499763489},{"id":"https://openalex.org/C96972482","wikidata":"https://www.wikidata.org/wiki/Q1049168","display_name":"Xeon Phi","level":2,"score":0.5023744106292725},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.49631911516189575},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.41687777638435364},{"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/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"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":"D003199","descriptor_name":"Computer Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003199","descriptor_name":"Computer Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003199","descriptor_name":"Computer Systems","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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty648","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty648","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/3/421/48965413/bioinformatics_35_3_421.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"pmh:oai:pubmedcentral.nih.gov:6361242","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6361242","pdf_url":null,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:30020410","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30020410","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:5356733","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6361242","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty648","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty648","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/3/421/48965413/bioinformatics_35_3_421.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":0.46000000834465027,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1742171491","display_name":null,"funder_award_id":"1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G179862484","display_name":null,"funder_award_id":"ACI1548562","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2206590661","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2278338973","display_name":"Hardening and Scaling Core Genomics Software","funder_award_id":"5r01gm118568-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3226045097","display_name":null,"funder_award_id":"ACI-1 548 562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3730782400","display_name":"XSEDE 2.0:  Integrating, Enabling and Enhancing National Cyberinfrastructure with Expanding Community Involvement","funder_award_id":"1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4298445392","display_name":null,"funder_award_id":"R01-GM118568","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6056929667","display_name":null,"funder_award_id":"1548562","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2952597168.pdf","grobid_xml":"https://content.openalex.org/works/W2952597168.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1536852470","https://openalex.org/W1971309371","https://openalex.org/W1980747862","https://openalex.org/W2001079689","https://openalex.org/W2009571806","https://openalex.org/W2025648894","https://openalex.org/W2069278684","https://openalex.org/W2095680943","https://openalex.org/W2102145367","https://openalex.org/W2102278945","https://openalex.org/W2104549677","https://openalex.org/W2104861744","https://openalex.org/W2108234281","https://openalex.org/W2117608012","https://openalex.org/W2122707695","https://openalex.org/W2124985265","https://openalex.org/W2131026689","https://openalex.org/W2131271579","https://openalex.org/W2133883933","https://openalex.org/W2133956160","https://openalex.org/W2142386149","https://openalex.org/W2143788241","https://openalex.org/W2159954944","https://openalex.org/W2170551349","https://openalex.org/W2198767643","https://openalex.org/W2254450385","https://openalex.org/W2288176647","https://openalex.org/W2323326409","https://openalex.org/W2619821731","https://openalex.org/W2727285297","https://openalex.org/W2746871167","https://openalex.org/W2951529834","https://openalex.org/W2952944477","https://openalex.org/W3136177209","https://openalex.org/W4230444879","https://openalex.org/W4394666350","https://openalex.org/W6674561012","https://openalex.org/W6679671437","https://openalex.org/W6681532532"],"related_works":["https://openalex.org/W2526069705","https://openalex.org/W2024016913","https://openalex.org/W2773471004","https://openalex.org/W2909639320","https://openalex.org/W2898398754","https://openalex.org/W3090309567","https://openalex.org/W88591960","https://openalex.org/W4241706480","https://openalex.org/W2035419609","https://openalex.org/W947442053"],"abstract_inverted_index":{"Motivation:":[0],"General-purpose":[1],"processors":[2],"can":[3],"now":[4],"contain":[5],"many":[6,80],"dozens":[7],"of":[8,14,17,23,40,68],"processor":[9],"cores":[10],"and":[11,32,42,72,103,111],"support":[12],"hundreds":[13],"simultaneous":[15],"threads":[16],"execution.":[18],"To":[19],"make":[20],"best":[21],"use":[22],"these":[24,41,63],"threads,":[25],"genomics":[26],"software":[27],"must":[28],"contend":[29],"with":[30],"new":[31,66],"subtle":[33],"computer":[34],"architecture":[35],"issues.":[36],"We":[37,61,74,90],"discuss":[38],"some":[39],"propose":[43],"methods":[44,64],"for":[45,114],"improving":[46],"thread":[47,77],"scaling":[48,78],"in":[49,65,79],"tools":[50],"that":[51,106],"analyze":[52],"each":[53],"read":[54,58],"independently,":[55],"such":[56],"as":[57],"aligners.":[59],"Results:":[60],"implement":[62],"versions":[67],"Bowtie,":[69],"Bowtie":[70,120],"2":[71],"HISAT.":[73],"greatly":[75],"improve":[76],"scenarios,":[81],"including":[82],"on":[83],"the":[84],"recent":[85],"Intel":[86],"Xeon":[87],"Phi":[88],"architecture.":[89],"also":[91],"highlight":[92],"how":[93],"bottlenecks":[94],"are":[95,129],"exacerbated":[96],"by":[97],"variable-record-length":[98],"file":[99],"formats":[100],"like":[101],"FASTQ":[102],"suggest":[104],"changes":[105],"enable":[107],"superior":[108],"scaling.":[109],"Availability":[110],"implementation:":[112],"Experiments":[113],"this":[115],"study:":[116],"https://github.com/BenLangmead/bowtie-scaling.":[117],"Bowtie:":[118],"http://bowtie-bio.sourceforge.net.":[119],"2:":[121],"http://bowtie-bio.sourceforge.net/bowtie2.":[122],"HISAT:":[123],"http://www.ccb.jhu.edu/software/hisat.":[124],"Supplementary":[125,127],"information:":[126],"data":[128],"available":[130],"at":[131],"Bioinformatics":[132],"online.":[133]},"counts_by_year":[{"year":2026,"cited_by_count":126},{"year":2025,"cited_by_count":210},{"year":2024,"cited_by_count":213},{"year":2023,"cited_by_count":168},{"year":2022,"cited_by_count":99},{"year":2021,"cited_by_count":116},{"year":2020,"cited_by_count":68},{"year":2019,"cited_by_count":26},{"year":2018,"cited_by_count":4}],"updated_date":"2026-09-02T07:38:04.252551","created_date":"2025-10-10T00:00:00"}
