{"id":"https://openalex.org/W2949847738","doi":"https://doi.org/10.1093/bioinformatics/btz169","title":"Holistic optimization of an RNA-seq workflow for multi-threaded environments","display_name":"Holistic optimization of an RNA-seq workflow for multi-threaded environments","publication_year":2019,"publication_date":"2019-03-09","ids":{"openalex":"https://openalex.org/W2949847738","doi":"https://doi.org/10.1093/bioinformatics/btz169","mag":"2949847738","pmid":"https://pubmed.ncbi.nlm.nih.gov/30859176"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz169","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz169","pdf_url":null,"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":null,"license_id":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6792127","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012172477","display_name":"Ling\u2010Hong Hung","orcid":"https://orcid.org/0000-0002-5209-2248"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ling-Hong Hung","raw_affiliation_strings":["School of Engineering and Technology , Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering and Technology , Tacoma, WA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021815916","display_name":"Wes Lloyd","orcid":"https://orcid.org/0000-0003-2021-8501"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wes Lloyd","raw_affiliation_strings":["School of Engineering and Technology , Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering and Technology , Tacoma, WA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009253920","display_name":"Radhika Agumbe Sridhar","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Radhika Agumbe Sridhar","raw_affiliation_strings":["School of Engineering and Technology , Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering and Technology , Tacoma, WA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086337627","display_name":"Saranya Devi Athmalingam Ravishankar","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Saranya Devi Athmalingam Ravishankar","raw_affiliation_strings":["School of Engineering and Technology , Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering and Technology , Tacoma, WA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073397841","display_name":"Yuguang Xiong","orcid":"https://orcid.org/0000-0001-6853-7443"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuguang Xiong","raw_affiliation_strings":["Ichahn School of Medicine at Mount Sinai , New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ichahn School of Medicine at Mount Sinai , New York, NY, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000485841","display_name":"Eric A. Sobie","orcid":"https://orcid.org/0000-0001-7327-8538"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Sobie","raw_affiliation_strings":["Ichahn School of Medicine at Mount Sinai , New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ichahn School of Medicine at Mount Sinai , New York, NY, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021881439","display_name":"Ka Yee Yeung","orcid":"https://orcid.org/0000-0002-1754-7577"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ka Yee Yeung","raw_affiliation_strings":["School of Engineering and Technology , Tacoma, WA, USA"],"raw_orcid":"https://orcid.org/0000-0002-1754-7577","affiliations":[{"raw_affiliation_string":"School of Engineering and Technology , Tacoma, WA, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5021881439"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4143,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60757599,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"20","first_page":"4173","last_page":"4175"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9785000085830688,"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":0.9785000085830688,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.00419999985024333,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.002300000051036477,"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":0.8526163101196289},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7588814496994019},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.6807258725166321},{"id":"https://openalex.org/keywords/thread","display_name":"Thread (computing)","score":0.5975317358970642},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5884725451469421},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5462042093276978},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.5448006987571716},{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.5415222644805908},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.5245604515075684},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5067937970161438},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.46602439880371094},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.4506422281265259},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41333240270614624},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3469281792640686},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3294448256492615},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3203672170639038},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2316933274269104}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8526163101196289},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7588814496994019},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6807258725166321},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.5975317358970642},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5884725451469421},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5462042093276978},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.5448006987571716},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.5415222644805908},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.5245604515075684},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5067937970161438},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.46602439880371094},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.4506422281265259},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41333240270614624},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3469281792640686},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3294448256492615},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3203672170639038},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2316933274269104}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz169","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz169","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30859176","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30859176","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:pubmedcentral.nih.gov:6792127","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6792127","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:6792127","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6792127","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.47999998927116394,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2777337649","display_name":null,"funder_award_id":"U54HL127624","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4113628564","display_name":null,"funder_award_id":"U54 HG008098","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4318098305","display_name":null,"funder_award_id":"R01 GM126019","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5521143350","display_name":null,"funder_award_id":"R01GM126019","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7375544220","display_name":null,"funder_award_id":"U54 HL127624","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W2084942072","https://openalex.org/W2103441770","https://openalex.org/W2118258530","https://openalex.org/W2150871235","https://openalex.org/W2169456326","https://openalex.org/W2172958821","https://openalex.org/W2323326409","https://openalex.org/W2592811885","https://openalex.org/W2949350745","https://openalex.org/W6684992291"],"related_works":["https://openalex.org/W3120493416","https://openalex.org/W2098192829","https://openalex.org/W3096946169","https://openalex.org/W2113128227","https://openalex.org/W4312114021","https://openalex.org/W2144610372","https://openalex.org/W4311938462","https://openalex.org/W2121840477","https://openalex.org/W2515936044","https://openalex.org/W3123068371"],"abstract_inverted_index":{"SUMMARY:":[0],"For":[1],"many":[2,63],"next":[3],"generation-sequencing":[4],"pipelines,":[5],"the":[6,12,27,41,58,112,123,131,141],"most":[7],"computationally":[8],"intensive":[9],"step":[10,133],"is":[11,30,35],"alignment":[13,23,132],"of":[14,76,84],"reads":[15],"to":[16,55],"a":[17,21,69,89,97,108,137],"reference":[18],"sequence.":[19],"As":[20],"result,":[22],"software":[24],"such":[25],"as":[26],"Burrows-Wheeler":[28],"Aligner":[29],"optimized":[31,54],"for":[32],"speed":[33,59,93],"and":[34,81,116,156,162],"often":[36],"executed":[37,95,102],"in":[38,92,135],"parallel":[39,114,143],"on":[40],"cloud.":[42],"However,":[43,100],"there":[44],"are":[45,158,171],"other":[46],"less":[47],"demanding":[48],"steps":[49,87],"that":[50],"can":[51],"also":[52],"be":[53],"significantly":[56],"increase":[57,91],"especially":[60],"when":[61,94,101],"using":[62,68,96,103,145],"threads.":[64,147],"We":[65],"demonstrate":[66],"this":[67],"unique":[70],"molecular":[71],"identifier":[72],"RNA-sequencing":[73],"pipeline":[74],"consisting":[75],"3":[77],"steps:":[78],"split,":[79],"align,":[80],"merge.":[82],"Optimization":[83],"all":[85],"three":[86],"yields":[88],"40%":[90],"single":[98],"thread.":[99],"16":[104,146],"threads,":[105],"we":[106],"observe":[107],"4-fold":[109],"improvement":[110,121,139],"over":[111,122,140],"original":[113,124,142],"implementation":[115],"more":[117],"than":[118],"an":[119],"8-fold":[120],"single-threaded":[125],"implementation.":[126],"In":[127],"contrast,":[128],"optimizing":[129],"only":[130],"results":[134],"just":[136],"13%":[138],"workflow":[144],"AVAILABILITY":[148],"AND":[149],"IMPLEMENTATION:":[150],"Code":[151],"(M.I.T.":[152],"license),":[153],"supporting":[154],"scripts":[155],"Dockerfiles":[157],"available":[159,172],"at":[160,165,173],"https://github.com/BioDepot/LINCS_RNAseq_cpp":[161],"Docker":[163],"images":[164],"https://hub.docker.com/r/biodepot/rnaseq-umi-cpp/.":[166],"SUPPLEMENTARY":[167],"INFORMATION:":[168],"Supplementary":[169],"data":[170],"Bioinformatics":[174],"online.":[175]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}