{"id":"https://openalex.org/W4313413299","doi":"https://doi.org/10.1109/bibm55620.2022.9995332","title":"RabbitQCPlus: More Efficient Quality Control for Sequencing Data","display_name":"RabbitQCPlus: More Efficient Quality Control for Sequencing Data","publication_year":2022,"publication_date":"2022-12-06","ids":{"openalex":"https://openalex.org/W4313413299","doi":"https://doi.org/10.1109/bibm55620.2022.9995332"},"language":"en","primary_location":{"id":"doi:10.1109/bibm55620.2022.9995332","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm55620.2022.9995332","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5072639624","display_name":"Lifeng Yan","orcid":"https://orcid.org/0000-0001-9610-1268"},"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":"Lifeng Yan","raw_affiliation_strings":["Shandong University,School of Software,Jinan,China","School of Software, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Software,Jinan,China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"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":["Shandong University,School of Software,Jinan,China","School of Software, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Software,Jinan,China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","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":["Shandong University,School of Software,Jinan,China","School of Software, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Software,Jinan,China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003236313","display_name":"Zhan Zhao","orcid":"https://orcid.org/0000-0001-5170-9608"},"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":"Zhan Zhao","raw_affiliation_strings":["Shandong University,School of Software,Jinan,China","School of Software, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Software,Jinan,China","institution_ids":["https://openalex.org/I154099455"]},{"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":["Shandong University,School of Software,Jinan,China","School of Software, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Software,Jinan,China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107834032","display_name":"Andr\u00e9 C. M\u00fcller","orcid":"https://orcid.org/0000-0002-0608-8176"},"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":"Andre Muller","raw_affiliation_strings":["Institute for Computer Science, Johannes Gutenberg University,Mainz","Institute for Computer Science, Johannes Gutenberg University, Mainz"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computer Science, Johannes Gutenberg University,Mainz","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Institute for Computer Science, Johannes Gutenberg University, Mainz","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043372390","display_name":"Robin Kobus","orcid":"https://orcid.org/0000-0003-2726-1908"},"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":"Robin Kobus","raw_affiliation_strings":["Institute for Computer Science, Johannes Gutenberg University,Mainz","Institute for Computer Science, Johannes Gutenberg University, Mainz"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computer Science, Johannes Gutenberg University,Mainz","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Institute for Computer Science, Johannes Gutenberg University, Mainz","institution_ids":["https://openalex.org/I197323543"]}]},{"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":["Shenzhen Institutes of Advanced Technology,Chinese Academy of Sciences,Shenzhen,China","Chinese Academy of Sciences, Shenzhen Institutes of Advanced Technology, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen Institutes of Advanced Technology,Chinese Academy of Sciences,Shenzhen,China","institution_ids":["https://openalex.org/I4210145761"]},{"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/A5008702128","display_name":"Beifang Niu","orcid":"https://orcid.org/0000-0002-7448-7793"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Beifang Niu","raw_affiliation_strings":["Chinese Academy of Sciences,Computer Network Information Center,Beijing,China","Computer Network Information Center, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences,Computer Network Information Center,Beijing,China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"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","Institute for Computer Science, Johannes Gutenberg University, Mainz"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computer Science, Johannes Gutenberg University,Mainz","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Institute for Computer Science, Johannes Gutenberg University, Mainz","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":["Shandong University,School of Software,Jinan,China","School of Software, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Software,Jinan,China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":11,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4283,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.52033195,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"619","last_page":"626"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9983000159263611,"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"}},"topics":[{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9983000159263611,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9970999956130981,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9711999893188477,"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/computer-science","display_name":"Computer science","score":0.8576071262359619},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.5649769306182861},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5325471758842468},{"id":"https://openalex.org/keywords/control","display_name":"Control (management)","score":0.5096790790557861},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5040549039840698},{"id":"https://openalex.org/keywords/external-data-representation","display_name":"External Data Representation","score":0.4644389748573303},{"id":"https://openalex.org/keywords/data-compression","display_name":"Data compression","score":0.4416513741016388},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3968431353569031},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3941173851490021},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1970376968383789},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.12293359637260437},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09275829792022705}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8576071262359619},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.5649769306182861},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5325471758842468},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.5096790790557861},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5040549039840698},{"id":"https://openalex.org/C116409475","wikidata":"https://www.wikidata.org/wiki/Q1385056","display_name":"External Data Representation","level":2,"score":0.4644389748573303},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.4416513741016388},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3968431353569031},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3941173851490021},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1970376968383789},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.12293359637260437},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09275829792022705},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm55620.2022.9995332","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm55620.2022.9995332","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321408","display_name":"Ministry of Education","ror":"https://ror.org/01p262204"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W2036897871","https://openalex.org/W2119180969","https://openalex.org/W2123845384","https://openalex.org/W2131271579","https://openalex.org/W2195724570","https://openalex.org/W2396849069","https://openalex.org/W2463091895","https://openalex.org/W2490087886","https://openalex.org/W2585711475","https://openalex.org/W2598066557","https://openalex.org/W2745824628","https://openalex.org/W2774072836","https://openalex.org/W2909529610","https://openalex.org/W2950464960","https://openalex.org/W2951278111","https://openalex.org/W2951912016","https://openalex.org/W2965891918","https://openalex.org/W3012532094","https://openalex.org/W3049347638","https://openalex.org/W3093528466","https://openalex.org/W6758282009"],"related_works":["https://openalex.org/W2917844847","https://openalex.org/W2036757537","https://openalex.org/W88681043","https://openalex.org/W2096451653","https://openalex.org/W4238546310","https://openalex.org/W4282930045","https://openalex.org/W4241634354","https://openalex.org/W2792082393","https://openalex.org/W2021866862","https://openalex.org/W2376367779"],"abstract_inverted_index":{"Assessing":[0],"the":[1,133],"quality":[2,30,42,76],"of":[3,114],"sequencing":[4,117],"data":[5,12,59],"plays":[6],"a":[7,128],"crucial":[8],"role":[9],"in":[10],"downstream":[11],"analysis.":[13,36,136],"However,":[14],"existing":[15],"tools":[16],"often":[17],"achieve":[18,62],"sub-optimal":[19],"efficiency,":[20],"especially":[21],"when":[22,73,99,131],"dealing":[23],"with":[24],"compressed":[25],"files":[26],"or":[27],"performing":[28,74],"complicated":[29],"control":[31,43,77],"operations":[32,78],"such":[33],"as":[34],"over-representation":[35,135],"We":[37],"present":[38],"RabbitQCPlus,":[39],"an":[40],"ultra-efficient":[41],"tool":[44],"for":[45],"modern":[46],"multi-core":[47],"systems.":[48],"RabbitQCPlus":[49,89],"uses":[50],"vectorization,":[51],"memory":[52],"copy":[53],"reduction,":[54],"parallel":[55],"(de)compression,":[56],"and":[57],"optimized":[58],"structures":[60],"to":[61,69,80,111],"substantial":[63],"performance":[64],"gains.":[65],"It":[66],"is":[67,90],"1.1":[68],"5.4":[70],"times":[71,94],"faster":[72,95],"basic":[75],"compared":[79],"state-of-the-art":[81],"applications":[82,98,121],"yet":[83],"requires":[84],"fewer":[85],"compute":[86],"resources.":[87],"Moreover,":[88],"at":[91,123,141],"least":[92,124],"4":[93,109],"than":[96,108],"other":[97,120],"processing":[100],"gzip-compressed":[101],"FASTQ":[102,116],"files.":[103],"Furthermore,":[104],"it":[105],"takes":[106],"less":[107],"minutes":[110,126],"process":[112],"280GB":[113],"plain":[115],"data,":[118],"while":[119],"take":[122],"22":[125],"on":[127],"48-core":[129],"server":[130],"enabling":[132],"per-read":[134],"C++":[137],"sources":[138],"are":[139],"available":[140],"https://github.com/RabbitBio/RabbitQCPlus.":[142]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}