{"id":"https://openalex.org/W4387848929","doi":"https://doi.org/10.1145/3583780.3615268","title":"Efficient Variant Calling on Human Genome Sequences Using a GPU-Enabled Commodity Cluster","display_name":"Efficient Variant Calling on Human Genome Sequences Using a GPU-Enabled Commodity Cluster","publication_year":2023,"publication_date":"2023-10-21","ids":{"openalex":"https://openalex.org/W4387848929","doi":"https://doi.org/10.1145/3583780.3615268"},"language":"en","primary_location":{"id":"doi:10.1145/3583780.3615268","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3583780.3615268","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 32nd ACM International Conference on Information and Knowledge Management","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/A5071075112","display_name":"Manas Jyoti Das","orcid":"https://orcid.org/0009-0007-9268-4364"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Manas Jyoti Das","raw_affiliation_strings":["University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066209865","display_name":"Khawar Shehzad","orcid":"https://orcid.org/0009-0007-1552-3161"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Khawar Shehzad","raw_affiliation_strings":["University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087950601","display_name":"Praveen Rao","orcid":"https://orcid.org/0000-0002-1859-0438"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Praveen Rao","raw_affiliation_strings":["University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071075112"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":0.4568,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.67761213,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"3843","last_page":"3848"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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":0.9983999729156494,"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/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9693999886512756,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical 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/T11478","display_name":"Caching and Content Delivery","score":0.9577999711036682,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/computer-science","display_name":"Computer science","score":0.8053773045539856},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7165987491607666},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5468693375587463},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5465244650840759},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5331883430480957},{"id":"https://openalex.org/keywords/server","display_name":"Server","score":0.49607691168785095},{"id":"https://openalex.org/keywords/workload","display_name":"Workload","score":0.4675276279449463},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.4422683119773865},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.43880751729011536},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.4223068654537201},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.24662742018699646},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12121298909187317},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10900530219078064}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8053773045539856},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7165987491607666},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5468693375587463},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5465244650840759},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5331883430480957},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.49607691168785095},{"id":"https://openalex.org/C2778476105","wikidata":"https://www.wikidata.org/wiki/Q628539","display_name":"Workload","level":2,"score":0.4675276279449463},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.4422683119773865},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.43880751729011536},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.4223068654537201},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.24662742018699646},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12121298909187317},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10900530219078064},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","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/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3583780.3615268","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3583780.3615268","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 32nd ACM International Conference on Information and Knowledge Management","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","score":0.7400000095367432,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G1290443700","display_name":null,"funder_award_id":"2201583","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1598064945","https://openalex.org/W1904861952","https://openalex.org/W1983587324","https://openalex.org/W2017928178","https://openalex.org/W2098935637","https://openalex.org/W2104846587","https://openalex.org/W2117798581","https://openalex.org/W2121762798","https://openalex.org/W2141978878","https://openalex.org/W2149059931","https://openalex.org/W2159670728","https://openalex.org/W2160363604","https://openalex.org/W2396849069","https://openalex.org/W2398924165","https://openalex.org/W2889664156","https://openalex.org/W3003307593","https://openalex.org/W3093528466","https://openalex.org/W3094438816","https://openalex.org/W3107396733","https://openalex.org/W3211269552","https://openalex.org/W4235230959","https://openalex.org/W4281384081"],"related_works":["https://openalex.org/W2000785801","https://openalex.org/W986318368","https://openalex.org/W2384410913","https://openalex.org/W2352878646","https://openalex.org/W2004734601","https://openalex.org/W2130149817","https://openalex.org/W2990194547","https://openalex.org/W1480123525","https://openalex.org/W2620865396","https://openalex.org/W2414054180"],"abstract_inverted_index":{"Human":[0],"genome":[1,29,161],"sequences":[2],"are":[3],"very":[4],"large":[5,64],"in":[6,44,101],"size":[7],"and":[8,12,17,47,149],"require":[9],"significant":[10],"compute":[11],"storage":[13],"resources":[14,100],"for":[15,57,111],"processing":[16,75],"analysis.":[18],"Variant":[19],"calling":[20,60],"is":[21],"a":[22,54,63,70,87,107,113,120,142],"key":[23],"task":[24],"performed":[25],"on":[26,62,96,116,141],"an":[27,170],"individual's":[28],"to":[30,41,90,169],"identify":[31],"different":[32,154],"types":[33,155],"of":[34,66,99,119,156],"variants.":[35],"Knowing":[36],"these":[37],"variants":[38],"can":[39,130],"lead":[40],"new":[42,55],"advances":[43],"disease":[45],"diagnosis":[46],"treatment.":[48],"In":[49],"this":[50],"work,":[51],"we":[52],"propose":[53],"approach":[56,79,140,164,171],"accelerating":[58],"variant":[59],"pipelines":[61],"workload":[65],"human":[67],"genomes":[68],"using":[69,133],"commodity":[71],"cluster":[72,121,144,176],"with":[73,145],"graphics":[74],"units":[76],"(GPUs).":[77],"Our":[78],"has":[80],"two":[81],"salient":[82],"features:":[83],"First,":[84],"it":[85,105],"enables":[86],"pipeline":[88,114],"stage":[89,115],"use":[91],"GPUs":[92,118],"and/or":[93],"CPUs":[94,134],"based":[95],"the":[97,102,117,125,175],"availability":[98],"cluster.":[103],"Second,":[104],"employs":[106],"mutual":[108],"exclusion":[109],"strategy":[110],"executing":[112],"node":[122],"so":[123],"that":[124,172],"stages":[126],"(for":[127],"other":[128],"sequences)":[129],"be":[131],"executed":[132],"if":[135],"needed.":[136],"We":[137],"evaluated":[138],"our":[139,163],"8-node":[143],"bare":[146],"metal":[147],"servers":[148],"virtual":[150],"machines":[151],"(VMs)":[152],"containing":[153],"GPUs.":[157],"On":[158],"publicly":[159],"available":[160],"sequences,":[162],"was":[165],"3.6X-5X":[166],"faster":[167],"compared":[168],"used":[173],"only":[174],"CPUs.":[177]},"counts_by_year":[{"year":2024,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
