{"id":"https://openalex.org/W4308187598","doi":"https://doi.org/10.1109/tcbb.2022.3219114","title":"RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms","display_name":"RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms","publication_year":2022,"publication_date":"2022-11-04","ids":{"openalex":"https://openalex.org/W4308187598","doi":"https://doi.org/10.1109/tcbb.2022.3219114","pmid":"https://pubmed.ncbi.nlm.nih.gov/36327193"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3219114","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3219114","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5100779648","display_name":"Hao Zhang","orcid":"https://orcid.org/0000-0001-9548-5239"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Zhang","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China"],"raw_orcid":"https://orcid.org/0000-0001-9548-5239","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111701379","display_name":"Honglei Song","orcid":null},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Honglei Song","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024616744","display_name":"XU Xiao-ming","orcid":"https://orcid.org/0000-0002-0370-2222"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoming Xu","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062588051","display_name":"Qixin Chang","orcid":"https://orcid.org/0000-0002-9140-8719"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qixin Chang","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008719586","display_name":"Mingkai Wang","orcid":"https://orcid.org/0000-0002-2882-0583"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingkai Wang","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037823825","display_name":"Yanjie Wei","orcid":"https://orcid.org/0000-0002-4791-7540"},"institutions":[{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanjie Wei","raw_affiliation_strings":["Chinese Academy of Sciences, Shenzhen Institutes of Advanced Technology, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Shenzhen Institutes of Advanced Technology, Shenzhen, China","institution_ids":["https://openalex.org/I4210145761"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091033464","display_name":"Zekun Yin","orcid":"https://orcid.org/0000-0001-6002-0028"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zekun Yin","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China"],"raw_orcid":"https://orcid.org/0000-0001-6002-0028","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"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/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Institute for Computer Science, Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":"https://orcid.org/0000-0003-2597-8331","affiliations":[{"raw_affiliation_string":"Institute for Computer Science, Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100620772","display_name":"Weiguo Liu","orcid":"https://orcid.org/0000-0001-8834-0453"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiguo Liu","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China"],"raw_orcid":"https://orcid.org/0000-0001-8834-0453","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.526,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.85610738,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"20","issue":"3","first_page":"2341","last_page":"2348"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9911999702453613,"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":0.9911999702453613,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9817000031471252,"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"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9807000160217285,"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/parsing","display_name":"Parsing","score":0.8300765752792358},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.680423378944397},{"id":"https://openalex.org/keywords/core","display_name":"Core (optical fiber)","score":0.6029582619667053},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.45112624764442444},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.40430140495300293},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.055355578660964966}],"concepts":[{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.8300765752792358},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.680423378944397},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.6029582619667053},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.45112624764442444},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.40430140495300293},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.055355578660964966}],"mesh":[{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2022.3219114","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3219114","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36327193","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36327193","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1831202063","display_name":null,"funder_award_id":"62102231","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3658485239","display_name":null,"funder_award_id":"ZR2021QF089","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G4140447210","display_name":"\u9762\u5411\u8d85\u5927\u89c4\u6a21\u77ed\u8bfb\u751f\u7269\u5e8f\u5217\u6570\u636e\u7684\u9ad8\u6027\u80fd\u5339\u914d\u7b97\u6cd5\u7814\u7a76","funder_award_id":"61972231","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1905818355","https://openalex.org/W1976369775","https://openalex.org/W2075996757","https://openalex.org/W2104846587","https://openalex.org/W2113679889","https://openalex.org/W2114792961","https://openalex.org/W2131271579","https://openalex.org/W2170551349","https://openalex.org/W2170747616","https://openalex.org/W2585711475","https://openalex.org/W2745994342","https://openalex.org/W2781268828","https://openalex.org/W2783165199","https://openalex.org/W2901438556","https://openalex.org/W2950150251","https://openalex.org/W2951912016","https://openalex.org/W2952597168","https://openalex.org/W2971559821","https://openalex.org/W2979985440","https://openalex.org/W2987650093","https://openalex.org/W2990618091","https://openalex.org/W3012532094","https://openalex.org/W3037322650","https://openalex.org/W3049347638","https://openalex.org/W3080156496","https://openalex.org/W4394666350","https://openalex.org/W6674561012"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"The":[0],"continuous":[1],"growth":[2],"of":[3,11,14,20,30,50,63,109,157,162,195],"generated":[4],"sequencing":[5,56,87],"data":[6,57,88],"leads":[7,159],"to":[8,25,42,131,160,173,199],"the":[9,28,48,61,155,174],"development":[10],"a":[12,78,103,193],"variety":[13,194],"associated":[15,202],"bioinformatics":[16],"tools.":[17],"However,":[18],"many":[19],"them":[21],"are":[22,36],"not":[23],"able":[24],"fully":[26],"exploit":[27,60],"resources":[29],"modern":[31,64,68,90],"multi-core":[32,91],"systems":[33],"since":[34],"they":[35],"bottlenecked":[37],"by":[38,101,107],"parsing":[39,55,105,135],"files":[40,100],"leading":[41],"slow":[43],"execution":[44],"times.":[45],"This":[46],"motivates":[47],"design":[49],"an":[51,110],"efficient":[52],"method":[53,106],"for":[54,67,84],"that":[58,122,154,186],"can":[59,94,123,188],"power":[62],"hardware,":[65],"especially":[66],"CPUs":[69],"with":[70],"fast":[71],"storage":[72],"devices.":[73],"We":[74],"have":[75,140],"developed":[76],"RabbitFX,":[77],"fast,":[79],"efficient,":[80],"and":[81,98,118,149,169],"easy-to-use":[82],"framework":[83],"processing":[85],"biological":[86],"on":[89,177],"platforms.":[92],"It":[93,204],"efficiently":[95],"read":[96],"FASTA":[97],"FASTQ":[99],"combining":[102],"lightweight":[104],"means":[108],"optimized":[111],"formatting":[112],"implementation.":[113],"Furthermore,":[114],"we":[115,139],"provide":[116],"user-friendly":[117],"modularized":[119],"C++":[120],"APIs":[121],"be":[124,189],"easily":[125,190],"integrated":[126,141,191],"into":[127,143,192],"applications":[128],"in":[129],"order":[130],"increase":[132],"their":[133],"file":[134],"speed.":[136],"As":[137],"proof-of-concept,":[138],"RabbitFX":[142,158,187],"three":[144],"I/O-intensive":[145],"applications:":[146],"fastp,":[147],"Ktrim,":[148],"Mash.":[150],"Our":[151],"evaluation":[152],"shows":[153],"inclusion":[156],"speedups":[161],"at":[163,210],"least":[164],"11.6":[165],"(6.6),":[166],"2.4":[167],"(2.4),":[168],"3.7":[170],"(3.2)":[171],"compared":[172],"original":[175],"versions":[176],"plain":[178],"(gzip-compressed)":[179],"files,":[180],"respectively.":[181],"These":[182],"case":[183],"studies":[184],"demonstrate":[185],"NGS":[196],"analysis":[197],"tools":[198],"significantly":[200],"reduce":[201],"runtimes.":[203],"is":[205],"open":[206],"source":[207],"software":[208],"available":[209],"https://github.com/RabbitBio/RabbitFX.":[211]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
