{"id":"https://openalex.org/W4385489284","doi":"https://doi.org/10.1109/compsac57700.2023.00288","title":"Porting the Variant Calling Pipeline for NGS data in cloud-HPC environment","display_name":"Porting the Variant Calling Pipeline for NGS data in cloud-HPC environment","publication_year":2023,"publication_date":"2023-06-01","ids":{"openalex":"https://openalex.org/W4385489284","doi":"https://doi.org/10.1109/compsac57700.2023.00288"},"language":"en","primary_location":{"id":"doi:10.1109/compsac57700.2023.00288","doi":"https://doi.org/10.1109/compsac57700.2023.00288","is_oa":false,"landing_page_url":"https://doi.org/10.1109/compsac57700.2023.00288","pdf_url":null,"source":{"id":"https://openalex.org/S4363607883","display_name":"IEEE Annual Computers, Software, and Applications Conference (COMPSAC)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE 47th Annual Computers, Software, and Applications Conference (COMPSAC)","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/2318/1919364","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014226084","display_name":"Alberto Mulone","orcid":"https://orcid.org/0009-0009-2600-613X","observed_orcids":["https://orcid.org/0009-0009-2600-613X"]},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alberto Mulone","raw_affiliation_strings":["University of Turin,Department of Computer Science,Turin,Italy","Department of Computer Science, University of Turin, Turin, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Turin,Department of Computer Science,Turin,Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Department of Computer Science, University of Turin, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036405743","display_name":"Sherine Awad","orcid":"https://orcid.org/0000-0002-8606-0674","observed_orcids":["https://orcid.org/0000-0002-8606-0674"]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210116691","display_name":"Wellcome/MRC Institute of Metabolic Science","ror":"https://ror.org/0264dxb48","country_code":"GB","type":"facility","lineage":["https://openalex.org/I241749","https://openalex.org/I2802466933","https://openalex.org/I4210087105","https://openalex.org/I4210116691","https://openalex.org/I87048295","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sherine Awad","raw_affiliation_strings":["University of Cambridge,Institute of Metabolic Science,Cambridge,United Kingdom","Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Cambridge,Institute of Metabolic Science,Cambridge,United Kingdom","institution_ids":["https://openalex.org/I241749","https://openalex.org/I4210116691"]},{"raw_affiliation_string":"Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000327522","display_name":"Davide Chiarugi","orcid":"https://orcid.org/0000-0003-2752-3189","observed_orcids":["https://orcid.org/0000-0003-2752-3189"]},"institutions":[{"id":"https://openalex.org/I4210130445","display_name":"Max Planck Institute for Human Cognitive and Brain Sciences","ror":"https://ror.org/0387jng26","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210130445"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Davide Chiarugi","raw_affiliation_strings":["Max Planck Institute for Human Cognitive and Brain Science,Research and Development Group - Computing and Databases Services,Leipzig,Germany","Research and Development Group - Computing and Databases Services, Max Planck Institute for Human Cognitive and Brain Science, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Human Cognitive and Brain Science,Research and Development Group - Computing and Databases Services,Leipzig,Germany","institution_ids":["https://openalex.org/I4210130445"]},{"raw_affiliation_string":"Research and Development Group - Computing and Databases Services, Max Planck Institute for Human Cognitive and Brain Science, Leipzig, Germany","institution_ids":["https://openalex.org/I4210130445"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089092418","display_name":"Marco Aldinucci","orcid":"https://orcid.org/0000-0001-8788-0829","observed_orcids":["https://orcid.org/0000-0001-8788-0829"]},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Aldinucci","raw_affiliation_strings":["University of Turin,Department of Computer Science,Turin,Italy","Department of Computer Science, University of Turin, Turin, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Turin,Department of Computer Science,Turin,Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Department of Computer Science, University of Turin, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.8717,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.90426604,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1858","last_page":"1863"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9613999724388123,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9613999724388123,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0215000007301569,"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/T10101","display_name":"Cloud Computing and Resource Management","score":0.004399999976158142,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/variant-calling","display_name":"variant calling","score":0.9369999766349792},{"id":"https://openalex.org/keywords/next-generation-sequencing","display_name":"next-generation sequencing","score":0.6949999928474426},{"id":"https://openalex.org/keywords/bioinformatics-pipeline","display_name":"bioinformatics pipeline","score":0.5609999895095825},{"id":"https://openalex.org/keywords/streamflow","display_name":"river discharge","score":0.8090000152587891},{"id":"https://openalex.org/keywords/snakemake","display_name":"Snakemake","score":0.9909999966621399},{"id":"https://openalex.org/keywords/workflow-management-systems","display_name":"workflow management systems","score":0.9380000233650208},{"id":"https://openalex.org/keywords/human-genetic-variation","display_name":"human genetic variation","score":0.6790000200271606},{"id":"https://openalex.org/keywords/pipeline-optimization","display_name":"pipeline optimization","score":0.6079999804496765},{"id":"https://openalex.org/keywords/covid-19-testing","display_name":"COVID-19 testing","score":0.5289999842643738}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8154952526092529},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7759745121002197},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7588531970977783},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.7446416616439819},{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.6978309750556946},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.6064021587371826},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.5401268601417542},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.4969072639942169},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.45422035455703735},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.4471406042575836},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3377187252044678},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2600199282169342},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.19960692524909973}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/compsac57700.2023.00288","doi":"https://doi.org/10.1109/compsac57700.2023.00288","is_oa":false,"landing_page_url":"https://doi.org/10.1109/compsac57700.2023.00288","pdf_url":null,"source":{"id":"https://openalex.org/S4363607883","display_name":"IEEE Annual Computers, Software, and Applications Conference (COMPSAC)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE 47th Annual Computers, Software, and Applications Conference (COMPSAC)","raw_type":"proceedings-article"},{"id":"pmh:oai:iris.unito.it:2318/1919364","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/2318/1919364","pdf_url":null,"source":{"id":"https://openalex.org/S4306400637","display_name":"Institutional Research Information System University of Turin (University of Turin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I55143463","host_organization_name":"University of Turin","host_organization_lineage":["https://openalex.org/I55143463"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:iris.unito.it:2318/1919364","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/2318/1919364","pdf_url":null,"source":{"id":"https://openalex.org/S4306400637","display_name":"Institutional Research Information System University of Turin (University of Turin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I55143463","host_organization_name":"University of Turin","host_organization_lineage":["https://openalex.org/I55143463"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"display_name":"Good health and well-being","score":0.8199999928474426,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1919257374","https://openalex.org/W1984068087","https://openalex.org/W2119180969","https://openalex.org/W2168133698","https://openalex.org/W2170551349","https://openalex.org/W2770095154","https://openalex.org/W2946894050","https://openalex.org/W2953517386","https://openalex.org/W3004534295","https://openalex.org/W3093528466","https://openalex.org/W3098100238","https://openalex.org/W3146289764","https://openalex.org/W4220661638","https://openalex.org/W4255738661","https://openalex.org/W6746163975"],"related_works":["https://openalex.org/W2375304607","https://openalex.org/W2391168633","https://openalex.org/W2035995658","https://openalex.org/W2353477037","https://openalex.org/W1574425962","https://openalex.org/W2385499106","https://openalex.org/W2354357087","https://openalex.org/W2352774566","https://openalex.org/W4243836028","https://openalex.org/W2376671203"],"abstract_inverted_index":{"In":[0],"recent":[1],"years":[2],"we":[3],"have":[4],"understood":[5],"the":[6,21,25,41,52,57,76,93,110],"importance":[7],"of":[8,60,75],"analyzing":[9],"and":[10,95,134],"sequencing":[11],"human":[12],"genetic":[13],"variation.":[14],"A":[15],"relevant":[16],"aspect":[17],"that":[18,98],"emerged":[19],"from":[20],"Covid-19":[22],"pandemic":[23],"was":[24],"need":[26],"to":[27,39,72,83,101],"obtain":[28],"results":[29],"very":[30],"quickly;":[31],"this":[32],"involved":[33],"using":[34],"High-Performance":[35],"Computing":[36],"(HPC)":[37],"environments":[38,80,133],"execute":[40,73],"Next":[42],"Generation":[43],"Sequencing":[44],"(NGS)":[45],"pipeline.":[46],"However,":[47],"HPC":[48,126],"is":[49],"not":[50],"always":[51],"most":[53],"suitable":[54],"environment":[55],"for":[56],"entire":[58],"execution":[59],"a":[61,102,138],"pipeline,":[62],"especially":[63],"when":[64],"it":[65],"involves":[66],"many":[67],"heterogeneous":[68],"tools.":[69],"The":[70],"ability":[71],"parts":[74],"pipeline":[77],"on":[78,109,131],"different":[79],"can":[81],"lead":[82],"higher":[84],"performance":[85,130],"but":[86],"also":[87,117],"cheaper":[88],"executions.":[89],"This":[90],"work":[91],"shows":[92],"design":[94],"optimization":[96],"process":[97],"led":[99],"us":[100],"state-of-the-art":[103],"Variant":[104],"Calling":[105],"hybrid":[106,139],"workflow":[107],"based":[108],"StreamFlow":[111,119],"Workflow":[112],"Management":[113],"System":[114],"(WfMS).":[115],"We":[116],"compare":[118],"with":[120,137],"Snakemake,":[121],"an":[122],"established":[123],"WfMS":[124],"targeting":[125],"facilities,":[127],"observing":[128],"comparable":[129],"single":[132],"satisfactory":[135],"improvements":[136],"cloud-HPC":[140],"configuration.":[141]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2026-10-05T09:50:58.205359","created_date":"2025-10-10T00:00:00"}
