{"id":"https://openalex.org/W4412872238","doi":"https://doi.org/10.1109/tcbbio.2025.3590412","title":"RabbitBAM: Accelerating BAM File Manipulation on Multi-Core Platforms","display_name":"RabbitBAM: Accelerating BAM File Manipulation on Multi-Core Platforms","publication_year":2025,"publication_date":"2025-07-18","ids":{"openalex":"https://openalex.org/W4412872238","doi":"https://doi.org/10.1109/tcbbio.2025.3590412","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811285"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3590412","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3590412","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE 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/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"]},{"id":"https://openalex.org/I97750245","display_name":"Software (Spain)","ror":"https://ror.org/02ethns06","country_code":"ES","type":"company","lineage":["https://openalex.org/I4210087817","https://openalex.org/I97750245"]}],"countries":["CN","ES"],"is_corresponding":true,"raw_author_name":"Lifeng Yan","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","School of Software, Shandong University, Jinan"],"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan","institution_ids":["https://openalex.org/I97750245","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"]},{"id":"https://openalex.org/I97750245","display_name":"Software (Spain)","ror":"https://ror.org/02ethns06","country_code":"ES","type":"company","lineage":["https://openalex.org/I4210087817","https://openalex.org/I97750245"]}],"countries":["CN","ES"],"is_corresponding":false,"raw_author_name":"Zhan Zhao","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","School of Software, Shandong University, Jinan"],"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan","institution_ids":["https://openalex.org/I97750245","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"]},{"id":"https://openalex.org/I97750245","display_name":"Software (Spain)","ror":"https://ror.org/02ethns06","country_code":"ES","type":"company","lineage":["https://openalex.org/I4210087817","https://openalex.org/I97750245"]}],"countries":["CN","ES"],"is_corresponding":false,"raw_author_name":"Zekun Yin","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","School of Software, Shandong University, Jinan"],"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan","institution_ids":["https://openalex.org/I97750245","https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100378795","display_name":"Tong Zhang","orcid":"https://orcid.org/0000-0002-6196-5602"},"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"]},{"id":"https://openalex.org/I97750245","display_name":"Software (Spain)","ror":"https://ror.org/02ethns06","country_code":"ES","type":"company","lineage":["https://openalex.org/I4210087817","https://openalex.org/I97750245"]}],"countries":["CN","ES"],"is_corresponding":false,"raw_author_name":"Tong Zhang","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","School of Software, Shandong University, Jinan"],"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan","institution_ids":["https://openalex.org/I97750245","https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107396440","display_name":"Yang Yang","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"]},{"id":"https://openalex.org/I97750245","display_name":"Software (Spain)","ror":"https://ror.org/02ethns06","country_code":"ES","type":"company","lineage":["https://openalex.org/I4210087817","https://openalex.org/I97750245"]}],"countries":["CN","ES"],"is_corresponding":false,"raw_author_name":"Yang Yang","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","School of Software, Shandong University, Jinan"],"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan","institution_ids":["https://openalex.org/I97750245","https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101064191","display_name":"Fangjin Zhu","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"]},{"id":"https://openalex.org/I97750245","display_name":"Software (Spain)","ror":"https://ror.org/02ethns06","country_code":"ES","type":"company","lineage":["https://openalex.org/I4210087817","https://openalex.org/I97750245"]}],"countries":["CN","ES"],"is_corresponding":false,"raw_author_name":"Fangjin Zhu","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","School of Software, Shandong University, Jinan"],"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan","institution_ids":["https://openalex.org/I97750245","https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003075115","display_name":"Xiaohui Duan","orcid":"https://orcid.org/0000-0002-1913-6683"},"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"]},{"id":"https://openalex.org/I97750245","display_name":"Software (Spain)","ror":"https://ror.org/02ethns06","country_code":"ES","type":"company","lineage":["https://openalex.org/I4210087817","https://openalex.org/I97750245"]}],"countries":["CN","ES"],"is_corresponding":false,"raw_author_name":"Xiaohui Duan","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","School of Software, Shandong University, Jinan"],"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan","institution_ids":["https://openalex.org/I97750245","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"],"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"]},{"id":"https://openalex.org/I97750245","display_name":"Software (Spain)","ror":"https://ror.org/02ethns06","country_code":"ES","type":"company","lineage":["https://openalex.org/I4210087817","https://openalex.org/I97750245"]}],"countries":["CN","ES"],"is_corresponding":false,"raw_author_name":"Weiguo Liu","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","School of Software, Shandong University, Jinan"],"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University, Jinan","institution_ids":["https://openalex.org/I97750245","https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5072639624"],"corresponding_institution_ids":["https://openalex.org/I154099455","https://openalex.org/I97750245"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.2065313,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"5","first_page":"2320","last_page":"2326"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.954200029373169,"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":0.954200029373169,"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/T11424","display_name":"Security and Verification in Computing","score":0.9476000070571899,"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/T11614","display_name":"Cloud Data Security Solutions","score":0.9473000168800354,"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/core","display_name":"Core (optical fiber)","score":0.6252005696296692},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5027172565460205},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.434664249420166},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.08194425702095032}],"concepts":[{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.6252005696296692},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5027172565460205},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.434664249420166},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.08194425702095032}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3590412","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3590412","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811285","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811285","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 transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"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"}],"funders":[{"id":"https://openalex.org/F4320312071","display_name":"Ministry of Education, Libya","ror":"https://ror.org/02w030k33"},{"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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1999113425","https://openalex.org/W2104005232","https://openalex.org/W2108234281","https://openalex.org/W2128505445","https://openalex.org/W2135216100","https://openalex.org/W2396849069","https://openalex.org/W2585711475","https://openalex.org/W2789843538","https://openalex.org/W2801006204","https://openalex.org/W2867868648","https://openalex.org/W2912526495","https://openalex.org/W2951912016","https://openalex.org/W3007172120","https://openalex.org/W3131055609","https://openalex.org/W3131443014","https://openalex.org/W4311803917","https://openalex.org/W4385295441"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"With":[0],"the":[1,7,48,94],"continuous":[2],"advancement":[3],"of":[4,9,31,51,96],"sequencing":[5,109,116],"technology,":[6],"scale":[8],"biological":[10],"data":[11,91,110,117],"has":[12],"rapidly":[13],"increased.":[14],"BAM":[15],"format,":[16],"widely":[17],"used":[18],"for":[19],"storing":[20],"aligned":[21],"sequence":[22],"data,":[23],"is":[24],"very":[25],"popular":[26],"due":[27],"to":[28,45,79,119,141],"its":[29],"ease":[30],"use":[32,95],"and":[33,75,83,100,111,133],"good":[34],"compression":[35],"ratio.":[36],"However,":[37],"existing":[38],"BAM-format":[39,68],"file":[40,69,130],"I/O":[41,70],"libraries":[42],"often":[43],"fail":[44],"fully":[46],"leverage":[47],"computational":[49],"power":[50],"modern":[52],"multi-core":[53],"platforms,":[54],"resulting":[55],"in":[56],"low":[57],"CPU":[58],"utilization.":[59],"To":[60],"address":[61],"this,":[62],"we":[63,88],"introduce":[64],"RabbitBAM,":[65,136],"a":[66],"fast":[67],"library.":[71],"RabbitBAM":[72,103],"employs":[73],"pre-parsing":[74],"parallel":[76,85],"parsing":[77,81],"techniques":[78],"eliminate":[80],"bottlenecks":[82],"improve":[84],"efficiency.":[86],"Additionally,":[87],"optimize":[89],"multi-threaded":[90],"handling":[92],"through":[93],"dedicated":[97],"lock-free":[98],"queues":[99],"memory":[101],"pools.":[102],"achieves":[104],"2.1-3.3x":[105],"speedups":[106,113,139],"on":[107,114],"next-generation":[108],"1-2.2x":[112],"third-generation":[115],"compared":[118,140],"state-of-the-art":[120],"SAMtools":[121],"(HTSlib).":[122],"We":[123],"also":[124],"present":[125],"two":[126],"case":[127],"studies":[128],"(BAM":[129],"quality":[131],"control":[132],"sorting)":[134],"using":[135],"demonstrating":[137],"1.4-2.4x":[138],"other":[142],"implementations.":[143]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
