{"id":"https://openalex.org/W7126048676","doi":"https://doi.org/10.1109/bibm66473.2025.11356060","title":"RapidAVA: Efficient All-vs-All Overlap Detection in HiFi Reads","display_name":"RapidAVA: Efficient All-vs-All Overlap Detection in HiFi Reads","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126048676","doi":"https://doi.org/10.1109/bibm66473.2025.11356060"},"language":"en","primary_location":{"id":"doi:10.1109/bibm66473.2025.11356060","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 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/A5108959033","display_name":"Yiran Cheng","orcid":null},"institutions":[{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Yiran Cheng","raw_affiliation_strings":["The Hong Kong University of Science and Technology"],"affiliations":[{"raw_affiliation_string":"The Hong Kong University of Science and Technology","institution_ids":["https://openalex.org/I200769079"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103926979","display_name":"Zhuoyang Chen","orcid":"https://orcid.org/0009-0007-1859-4571"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhuoyang Chen","raw_affiliation_strings":["The Hong Kong University of Science and Technology (Guangzhou)"],"affiliations":[{"raw_affiliation_string":"The Hong Kong University of Science and Technology (Guangzhou)","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034823616","display_name":"Qiong Luo","orcid":"https://orcid.org/0000-0002-2861-9492"},"institutions":[{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Qiong Luo","raw_affiliation_strings":["The Hong Kong University of Science and Technology"],"affiliations":[{"raw_affiliation_string":"The Hong Kong University of Science and Technology","institution_ids":["https://openalex.org/I200769079"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5108959033"],"corresponding_institution_ids":["https://openalex.org/I200769079"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.64267385,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1602","last_page":"1607"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7523999810218811,"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":0.7523999810218811,"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":0.03500000014901161,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.027000000700354576,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/heuristics","display_name":"Heuristics","score":0.578000009059906},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5590999722480774},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.46140000224113464},{"id":"https://openalex.org/keywords/computational-complexity-theory","display_name":"Computational complexity theory","score":0.44699999690055847},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.43479999899864197},{"id":"https://openalex.org/keywords/wavefront","display_name":"Wavefront","score":0.322299987077713},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.3221000134944916}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7369999885559082},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.578000009059906},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5590999722480774},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.534500002861023},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.46140000224113464},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.44699999690055847},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.43479999899864197},{"id":"https://openalex.org/C165699331","wikidata":"https://www.wikidata.org/wiki/Q461533","display_name":"Wavefront","level":2,"score":0.322299987077713},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.3221000134944916},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.30559998750686646},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2816999852657318},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.2720000147819519},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2712000012397766},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2669999897480011},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.25440001487731934}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356060","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:repository.hkust.edu.hk:1783.1-170516","is_oa":false,"landing_page_url":"http://repository.hkust.edu.hk/ir/Record/1783.1-170516","pdf_url":null,"source":{"id":"https://openalex.org/S4306401796","display_name":"Rare & Special e-Zone (The Hong Kong University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200769079","host_organization_name":"Hong Kong University of Science and Technology","host_organization_lineage":["https://openalex.org/I200769079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Conference paper"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W344138311","https://openalex.org/W2107772251","https://openalex.org/W2125266506","https://openalex.org/W2144560237","https://openalex.org/W2194172909","https://openalex.org/W2566610827","https://openalex.org/W2625594140","https://openalex.org/W2755804176","https://openalex.org/W2789843538","https://openalex.org/W2950354111","https://openalex.org/W2950629094","https://openalex.org/W2964045878","https://openalex.org/W2968499116","https://openalex.org/W2992976869","https://openalex.org/W3047598142","https://openalex.org/W3086678357","https://openalex.org/W3115745540","https://openalex.org/W3200242814","https://openalex.org/W3216997764","https://openalex.org/W4226179456","https://openalex.org/W4310786235","https://openalex.org/W4390501810","https://openalex.org/W4390971119","https://openalex.org/W4400910556","https://openalex.org/W4406238208","https://openalex.org/W4406261579"],"related_works":[],"abstract_inverted_index":{"The":[0],"High-Fidelity":[1],"(HiFi)":[2],"sequencing":[3],"technology":[4],"produces":[5],"long,":[6],"highly":[7],"accurate":[8],"reads,":[9,39],"leading":[10],"to":[11,107,119,125],"higher-quality":[12],"results":[13],"in":[14,64],"genome":[15],"assembly.":[16],"All-vs-all":[17],"overlap":[18,62,83],"detection":[19,63],"is":[20],"an":[21],"important":[22],"task":[23],"for":[24,37,44,60,82,135,151],"de":[25],"novo":[26],"assembly":[27],"and":[28,48,144,169,177],"other":[29,140,192],"genomics":[30],"applications.":[31],"However,":[32],"existing":[33,160],"methods":[34],"remain":[35],"inefficient":[36],"HiFi":[38,65,152],"as":[40,80],"they":[41],"lack":[42],"optimizations":[43],"long":[45],"read":[46],"length":[47],"high":[49],"accuracy.":[50],"To":[51],"improve":[52,145],"efficiency,":[53],"we":[54,68,85,101,128],"introduce":[55],"RapidAVA,":[56],"a":[57,70,103,114,121],"new":[58],"method":[59],"all-vs-all":[61],"reads.":[66,99,117,153],"First,":[67],"identify":[69,126],"set":[71],"of":[72,90,97,116,123,164,190],"representative":[73],"subsequences,":[74],"or":[75],"minimizers,":[76],"from":[77],"all":[78],"reads":[79,124],"indices":[81],"detection;":[84],"keep":[86],"the":[87,98,109,130,146,191],"total":[88],"number":[89],"minimizers":[91,111],"small":[92],"while":[93],"ensuring":[94],"their":[95],"coverage":[96],"Second,":[100],"develop":[102],"fast":[104],"seed-chaining":[105],"algorithm":[106,134,147],"link":[108],"common":[110],"(seeds)":[112],"between":[113],"pair":[115,122],"Last,":[118],"align":[120],"overlap,":[127],"adopt":[129],"wavefront":[131],"alignment":[132],"(WFA)":[133],"its":[136,181],"lower":[137],"complexity":[138],"than":[139],"dynamic":[141],"programming":[142],"algorithms,":[143],"with":[148,180],"heuristics":[149],"suitable":[150],"Our":[154],"experiments":[155],"show":[156],"that":[157],"RapidAVA":[158],"outperforms":[159],"tools,":[161],"achieving":[162],"speedups":[163],"<tex":[165,170],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[166,171],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$4.7":[167],"\\times$</tex>":[168,173],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$2.3":[172],"over":[174],"Minimap":[175],"2":[176],"Hifiasm,":[178],"respectively,":[179],"peak":[182],"memory":[183],"consumption":[184],"at":[185],"13":[186],"-":[187],"50":[188],"%":[189],"systems.":[193]},"counts_by_year":[],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2026-01-30T00:00:00"}
