{"id":"https://openalex.org/W2902786278","doi":"https://doi.org/10.4233/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","title":"Accelerating DNA Variant Calling Algorithms on High Performance Computing Systems","display_name":"Accelerating DNA Variant Calling Algorithms on High Performance Computing Systems","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2902786278","doi":"https://doi.org/10.4233/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","mag":"2902786278"},"language":"en","primary_location":{"id":"pmh:oai:tudelft.nl:uuid:1752b8ce-631b-4127-91c9-92538e34a13b","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","pdf_url":"http://resolver.tudelft.nl/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doctoral thesis"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://resolver.tudelft.nl/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025656955","display_name":"Siying Ren","orcid":"https://orcid.org/0000-0001-6618-690X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ren, S.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5025656955"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9883000254631042,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9883000254631042,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9825000166893005,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9822999835014343,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/bottleneck","display_name":"Bottleneck","score":0.7704131603240967},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7520228624343872},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7356319427490234},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.567405104637146},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5389742255210876},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5089969635009766},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5034789443016052},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.49557673931121826},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4502614140510559},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.42990005016326904},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4160701036453247},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.1885669231414795},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.11711278557777405},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.10935688018798828},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10736474394798279}],"concepts":[{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7704131603240967},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7520228624343872},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7356319427490234},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.567405104637146},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5389742255210876},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5089969635009766},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5034789443016052},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.49557673931121826},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4502614140510559},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.42990005016326904},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4160701036453247},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.1885669231414795},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.11711278557777405},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.10935688018798828},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10736474394798279},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:tudelft.nl:uuid:1752b8ce-631b-4127-91c9-92538e34a13b","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","pdf_url":"http://resolver.tudelft.nl/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doctoral thesis"},{"id":"doi:10.4233/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","is_oa":true,"landing_page_url":"https://doi.org/10.4233/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","pdf_url":null,"source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"thesis"},{"id":"mag:2902786278","is_oa":false,"landing_page_url":"https://www.narcis.nl/publication/RecordID/oai:tudelft.nl:uuid%3A1752b8ce-631b-4127-91c9-92538e34a13b","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:tudelft.nl:uuid:1752b8ce-631b-4127-91c9-92538e34a13b","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","pdf_url":"http://resolver.tudelft.nl/uuid:1752b8ce-631b-4127-91c9-92538e34a13b","source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doctoral thesis"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.5099999904632568,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G6435145259","display_name":"Algorithms, Design Methods, and Many-Core Execution Platform for Low-Power Massive Data-Rate Video and Image Processing","funder_award_id":"621439","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/F4320321012","display_name":"Technische Universiteit Delft","ror":"https://ror.org/02e2c7k09"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2902786278.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3157025177","https://openalex.org/W2584732844","https://openalex.org/W2309105422","https://openalex.org/W2063257142","https://openalex.org/W77511975","https://openalex.org/W3167680374","https://openalex.org/W3004006192","https://openalex.org/W1585350690","https://openalex.org/W2741602961","https://openalex.org/W3115410382","https://openalex.org/W2035565732","https://openalex.org/W2483136543","https://openalex.org/W2106834352","https://openalex.org/W2770405949","https://openalex.org/W2063315665","https://openalex.org/W2164045449","https://openalex.org/W2901683642","https://openalex.org/W3006340603","https://openalex.org/W3045744481","https://openalex.org/W2898051748"],"abstract_inverted_index":{"Next":[0],"generation":[1],"sequencing":[2,20,45,57],"(NGS)":[3],"technologies":[4],"have":[5,35,109],"transformed":[6],"the":[7,13,43,52,66,69,72,79,136,142,174,183,188,201,209,243,253,262,270,281,285,291,301,313,327,335,339,359,369,378,387,409,413,423,432,472,485,489,494,507],"landscape":[8],"of":[9,55,71,130,141,200,216,226,284,312,326,338,346,412,452,488],"genomic":[10],"research.":[11],"With":[12],"significant":[14],"advances":[15],"in":[16,114,467,477,512],"NGS":[17,49],"technologies,":[18],"DNA":[19,31,73,92,159],"is":[21,155,256,381,428,444,503],"more":[22,449],"affordable":[23],"and":[24,103,124,187,223,396],"accessible":[25],"than":[26,261,386,431,506],"ever":[27],"before.":[28],"Meanwhile,":[29],"many":[30,115],"sequence":[32,74,93,160,362],"analysis":[33,75,161],"tools":[34],"been":[36],"developed":[37],"to":[38,78,126,149,218,228,241,258,267,279,298,310,348,357,367,383,446,465],"derive":[39],"useful":[40],"information":[41],"from":[42],"raw":[44],"data":[46,58],"produced":[47],"by":[48],"platforms.":[50],"However,":[51],"massive":[53],"amount":[54],"generated":[56],"poses":[59],"a":[60,128,156,196,214,224,237,277,295,317,344,440,448],"great":[61],"computational":[62,81,112],"challenge,":[63],"thereby":[64],"shifting":[65],"bottleneck":[67],"towards":[68],"efficiency":[70],"tools.":[76],"Due":[77],"high":[80,83,116],"needs,":[82],"performance":[84,117,282],"systems":[85],"are":[86,171],"playing":[87],"an":[88],"important":[89,111,131],"role":[90],"for":[91,181,205,316],"analysis.":[94],"Moreover,":[95],"dedicated":[96],"hardware,":[97],"including":[98,173],"graphics":[99],"processing":[100],"units":[101],"(GPUs)":[102],"field":[104],"programmable":[105],"gate":[106],"arrays":[107],"(FPGAs),":[108],"become":[110],"resources":[113,272,303],"systems.<br/>In":[118],"this":[119,501],"thesis,":[120],"we":[121,147,275,293,321,355,398,482],"use":[122,148],"GPUs":[123,395],"FPGAs":[125],"accelerate":[127,242,358],"number":[129],"bioinformatics":[132],"algorithms.":[133],"These":[134],"represent":[135],"most":[137],"computationally":[138,168],"intensive":[139,169],"algorithms":[140,170,393],"GATK":[143,153,165,404,418,425,434,460,474,495,509],"HaplotypeCaller":[144],"(HC),":[145],"which":[146],"improve":[150],"its":[151],"performance.":[152],"HC":[154,426,435,461,475,510],"widely":[157],"used":[158],"tool.":[162],"By":[163],"investigating":[164],"HC,":[166],"three":[167],"selected,":[172],"de":[175],"Buijn":[176],"graph":[177],"(DBG)":[178],"construction":[179,203],"algorithm":[180,186,204,246,342,364,416,492],"micro-assembly,":[182],"pair-HMMs":[184,244,328,340,414],"forward":[185,245,329,341,415],"semi-global":[189,360,490],"pairwise":[190,361],"alignment":[191,363,371,491],"algorithm.":[192,330],"We":[193,234,406],"first":[194,407],"propose":[195,236,294,322,356],"novel":[197,296],"GPU-based":[198,324,336,352,379,401,410,424,459,486],"implementation":[199,255,307,380,411,427,462,476,487,502,511],"DBG":[202],"micro-assembly.":[206],"Compared":[207],"with":[208,365],"software-only":[210,263,388],"implementation,":[211],"it":[212],"achieves":[213,308,463],"speedup":[215,225,345],"up":[217,227,257,309,347,382,464],"3x":[219],"using":[220,230],"synthetic":[221],"datasets":[222],"2.66x":[229],"human":[231],"genome":[232],"datasets.":[233],"then":[235],"systolic":[238,286],"array":[239,287],"design":[240],"on":[247,273,290,304,372,394],"FPGAs.":[248,305],"Experimental":[249,331,374,497],"results":[250,332,375,498],"show":[251,333,376],"that":[252,334,377,500],"FPGA-based":[254],"67x":[259],"faster":[260,385,430,505],"implementation.":[264,389,436],"In":[265,420],"order":[266],"fully":[268],"utilize":[269,300],"computing":[271,302],"FPGAs,":[274,397],"present":[276],"model":[278],"describe":[280],"characteristics":[283],"design.":[288],"Based":[289],"analysis,":[292],"architecture":[297],"better":[299],"The":[306,458],"90\\\\%":[311],"theoretical":[314],"throughput":[315],"real":[318],"dataset.":[319],"Next,":[320,481],"several":[323],"implementations":[325,337,402],"achieve":[343],"5.47x":[349],"over":[350,471],"existing":[351],"implementations.":[353],"Finally,":[354],"traceback":[366],"obtain":[368],"optimal":[370],"GPUs.":[373],"14.14x":[384],"<br/>After":[390],"accelerating":[391],"these":[392],"integrate":[399,408],"two":[400],"into":[403,417,493],"HC.":[405,419,496],"single-threaded":[421],"mode,":[422,439],"1.71x":[429],"baseline":[433,473,508],"For":[437],"multi-process":[438,442,469,479],"load-balanced":[441,468],"optimization":[443],"proposed":[445],"ensure":[447],"equal":[450],"distribution":[451],"computation":[453],"load":[454],"between":[455],"different":[456],"processes.":[457],"2.04x":[466],"mode":[470],"non-load-balanced":[478],"mode.":[480,514],"additionally":[483],"integrated":[484],"shown":[499],"2.3x":[504],"single-thread":[513]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2025-10-10T00:00:00"}