{"id":"https://openalex.org/W2054226908","doi":"https://doi.org/10.1186/1471-2105-12-85","title":"DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI","display_name":"DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI","publication_year":2011,"publication_date":"2011-03-29","ids":{"openalex":"https://openalex.org/W2054226908","doi":"https://doi.org/10.1186/1471-2105-12-85","mag":"2054226908","pmid":"https://pubmed.ncbi.nlm.nih.gov/21447171"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-85","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-85","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-85","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-85","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100617992","display_name":"Yongchao Liu","orcid":"https://orcid.org/0000-0003-3440-9675"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Yongchao Liu","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, 639798, Singapore. liuy0039@ntu.edu.sg","School of Computer Engineering, Nanyang Technological University,,Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, 639798, Singapore. liuy0039@ntu.edu.sg","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University,,Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, 639798, Singapore","School of Computer Engineering, Nanyang Technological University,,Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, 639798, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University,,Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059218594","display_name":"Douglas L. Maskell","orcid":"https://orcid.org/0000-0002-6588-4762"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Douglas L Maskell","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, 639798, Singapore","School of Computer Engineering, Nanyang Technological University,,Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, 639798, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University,,Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100617992"],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":8.6488,"has_fulltext":true,"cited_by_count":63,"citation_normalized_percentile":{"value":0.98014666,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"12","issue":"1","first_page":"85","last_page":"85"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.45739999413490295,"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"}},"topics":[{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.45739999413490295,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2989000082015991,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.065700002014637,"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":0.8566494584083557},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.8288925886154175},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7778710126876831},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6473487615585327},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.5952310562133789},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.5223948955535889},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.4743277430534363},{"id":"https://openalex.org/keywords/error-detection-and-correction","display_name":"Error detection and correction","score":0.4165096879005432},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.3087281286716461},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3071783781051636}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8566494584083557},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.8288925886154175},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7778710126876831},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6473487615585327},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.5952310562133789},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.5223948955535889},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.4743277430534363},{"id":"https://openalex.org/C103088060","wikidata":"https://www.wikidata.org/wiki/Q1062839","display_name":"Error detection and correction","level":2,"score":0.4165096879005432},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.3087281286716461},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3071783781051636},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-12-85","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-85","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-85","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21447171","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21447171","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:9a2c4d6d0fa747b39a724e218d70d995","is_oa":true,"landing_page_url":"https://doaj.org/article/9a2c4d6d0fa747b39a724e218d70d995","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 85 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2083893","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3072957","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-85","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-85","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-85","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4399999976158142,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2054226908.pdf","grobid_xml":"https://content.openalex.org/works/W2054226908.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1635391495","https://openalex.org/W1966822396","https://openalex.org/W1970339312","https://openalex.org/W1984021931","https://openalex.org/W2013733655","https://openalex.org/W2028499920","https://openalex.org/W2046594687","https://openalex.org/W2071116416","https://openalex.org/W2118335502","https://openalex.org/W2123845384","https://openalex.org/W2124985265","https://openalex.org/W2126540423","https://openalex.org/W2127651281","https://openalex.org/W2133540884","https://openalex.org/W2136651963","https://openalex.org/W2141217788","https://openalex.org/W2142702487","https://openalex.org/W2142749416","https://openalex.org/W2144662851","https://openalex.org/W2151017710","https://openalex.org/W2152246890","https://openalex.org/W2155503253","https://openalex.org/W2159998739","https://openalex.org/W2160969485","https://openalex.org/W2161546116","https://openalex.org/W2170896626","https://openalex.org/W2171475724","https://openalex.org/W2755087487","https://openalex.org/W3138798301","https://openalex.org/W4250730716","https://openalex.org/W4251237680"],"related_works":["https://openalex.org/W2075046026","https://openalex.org/W2142485291","https://openalex.org/W2037631693","https://openalex.org/W2319727539","https://openalex.org/W2152038948","https://openalex.org/W189420351","https://openalex.org/W2129161768","https://openalex.org/W2029040955","https://openalex.org/W2008492897","https://openalex.org/W127524933"],"abstract_inverted_index":{"BACKGROUND:":[0],"Next-generation":[1],"sequencing":[2,244],"technologies":[3],"have":[4],"led":[5],"to":[6,124,173,198,234],"the":[7,36,56,87,96,104,110,126,130,147,174,186,193,236],"high-throughput":[8,65],"production":[9],"of":[10,42,73,109,138,150,166,195,238],"sequence":[11],"data":[12],"(reads)":[13],"at":[14],"low":[15],"cost.":[16],"However,":[17],"these":[18],"reads":[19,67,240],"are":[20],"significantly":[21],"shorter":[22],"and":[23,45,59,75,83,92,98,103,112,117,132,144,156,170,184,189,218,229],"more":[24],"error-prone":[25],"than":[26],"conventional":[27],"Sanger":[28],"shotgun":[29],"reads.":[30],"This":[31],"poses":[32],"a":[33,70,119],"challenge":[34],"for":[35,47,64,146,204],"de":[37,200],"novo":[38,201],"assembly":[39,43,202],"in":[40,164,215],"terms":[41,165],"quality":[44,169,203],"scalability":[46],"large-scale":[48,151],"short":[49,66,239],"read":[50],"datasets.":[51,153],"RESULTS:":[52],"We":[53],"present":[54],"DecGPU,":[55],"first":[57],"parallel":[58,77,100,114],"distributed":[60,136],"error":[61,148,167,176,231],"correction":[62,149,168,177,232],"algorithm":[63,140,160,197,233],"(HTSRs)":[68],"using":[69,95],"hybrid":[71,120],"combination":[72],"CUDA":[74,111,216],"MPI":[76,97,113],"programming":[78,101,115],"models.":[79],"DecGPU":[80,208,225],"provides":[81],"CPU-based":[82,88],"GPU-based":[84,105],"versions,":[85],"where":[86],"version":[89,106],"employs":[90,118],"coarse-grained":[91],"fine-grained":[93],"parallelism":[94],"OpenMP":[99],"models,":[102],"takes":[107],"advantage":[108],"models":[116],"CPU+GPU":[121],"computing":[122],"model":[123],"maximize":[125],"performance":[127],"by":[128,242],"overlapping":[129],"CPU":[131],"GPU":[133],"computation.":[134],"The":[135,220],"feature":[137],"our":[139,159,196],"makes":[141],"it":[142],"feasible":[143,230],"flexible":[145],"HTSR":[152],"Using":[154],"simulated":[155],"real":[157],"datasets,":[158],"demonstrates":[161],"superior":[162],"performance,":[163],"execution":[171],"speed,":[172],"existing":[175],"algorithms.":[178],"Furthermore,":[179],"when":[180],"combined":[181],"with":[182],"Velvet":[183],"ABySS,":[185],"resulting":[187],"DecGPU-Velvet":[188],"DecGPU-ABySS":[190],"assemblers":[191],"demonstrate":[192],"potential":[194],"improve":[199],"de-Bruijn-graph-based":[205],"assemblers.":[206],"CONCLUSIONS:":[207],"is":[209,226],"publicly":[210],"available":[211],"open-source":[212],"software,":[213],"written":[214],"C++":[217],"MPI.":[219],"experimental":[221],"results":[222],"suggest":[223],"that":[224],"an":[227],"effective":[228],"tackle":[235],"flood":[237],"produced":[241],"next-generation":[243],"technologies.":[245]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":9}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
