{"id":"https://openalex.org/W4206696993","doi":"https://doi.org/10.1145/3473258.3473279","title":"Frigate: a fast, in-memory tool for counting and querying k-mers","display_name":"Frigate: a fast, in-memory tool for counting and querying k-mers","publication_year":2021,"publication_date":"2021-05-21","ids":{"openalex":"https://openalex.org/W4206696993","doi":"https://doi.org/10.1145/3473258.3473279"},"language":"en","primary_location":{"id":"doi:10.1145/3473258.3473279","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3473258.3473279","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 13th International Conference on Bioinformatics and Biomedical Technology","raw_type":"proceedings-article"},"type":"conference-paper","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/A5039160915","display_name":"Gunavaran Brihadiswaran","orcid":"https://orcid.org/0000-0002-4086-3607"},"institutions":[{"id":"https://openalex.org/I195740183","display_name":"University of Moratuwa","ror":"https://ror.org/0491f5305","country_code":"LK","type":"education","lineage":["https://openalex.org/I195740183"]}],"countries":["LK"],"is_corresponding":false,"raw_author_name":"Gunavaran Brihadiswaran","raw_affiliation_strings":["University of Moratuwa, Sri Lanka"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Moratuwa, Sri Lanka","institution_ids":["https://openalex.org/I195740183"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046054771","display_name":"Sanath Jayasena","orcid":"https://orcid.org/0000-0001-5097-8769"},"institutions":[{"id":"https://openalex.org/I195740183","display_name":"University of Moratuwa","ror":"https://ror.org/0491f5305","country_code":"LK","type":"education","lineage":["https://openalex.org/I195740183"]}],"countries":["LK"],"is_corresponding":false,"raw_author_name":"Sanath Jayasena","raw_affiliation_strings":["University of Moratuwa, Sri Lanka"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Moratuwa, Sri Lanka","institution_ids":["https://openalex.org/I195740183"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I195740183"],"apc_list":null,"apc_paid":null,"fwci":0.9389,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.7943284,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"134","last_page":"140"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9934999942779541,"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":0.9934999942779541,"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":0.9871000051498413,"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/T11478","display_name":"Caching and Content Delivery","score":0.984499990940094,"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/k-mer","display_name":"k-mer","score":0.8849368691444397},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7953009605407715},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7302334904670715},{"id":"https://openalex.org/keywords/lock","display_name":"Lock (firearm)","score":0.5905638337135315},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5695730447769165},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.49598345160484314},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.4870436489582062},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.4533483386039734},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.4274788796901703},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.41149306297302246},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3999709188938141},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34275928139686584},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.15692690014839172},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1462719738483429},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08867618441581726}],"concepts":[{"id":"https://openalex.org/C2279292","wikidata":"https://www.wikidata.org/wiki/Q6322851","display_name":"k-mer","level":4,"score":0.8849368691444397},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7953009605407715},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7302334904670715},{"id":"https://openalex.org/C174839445","wikidata":"https://www.wikidata.org/wiki/Q1134386","display_name":"Lock (firearm)","level":2,"score":0.5905638337135315},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5695730447769165},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.49598345160484314},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.4870436489582062},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.4533483386039734},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.4274788796901703},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.41149306297302246},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3999709188938141},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34275928139686584},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.15692690014839172},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1462719738483429},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08867618441581726},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3473258.3473279","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3473258.3473279","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 13th International Conference on Bioinformatics and Biomedical Technology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W2014099509","https://openalex.org/W2027667941","https://openalex.org/W2041391522","https://openalex.org/W2057253402","https://openalex.org/W2060380866","https://openalex.org/W2096128575","https://openalex.org/W2115501618","https://openalex.org/W2125266506","https://openalex.org/W2132926880","https://openalex.org/W2133956160","https://openalex.org/W2144268209","https://openalex.org/W2144560237","https://openalex.org/W2163584430","https://openalex.org/W2171888576","https://openalex.org/W2188584922","https://openalex.org/W2583363792","https://openalex.org/W2597444305","https://openalex.org/W2731118616","https://openalex.org/W2889313110","https://openalex.org/W2897927784","https://openalex.org/W2963173114","https://openalex.org/W2998976928"],"related_works":["https://openalex.org/W2484133401","https://openalex.org/W2115501618","https://openalex.org/W4297665144","https://openalex.org/W2127768708","https://openalex.org/W2013652688","https://openalex.org/W2163830511","https://openalex.org/W2061214760","https://openalex.org/W2159998739","https://openalex.org/W2268029186","https://openalex.org/W2165847428"],"abstract_inverted_index":{"K-mer":[0],"counting":[1,57],"is":[2,36],"an":[3],"important":[4],"step":[5],"in":[6,22,29],"many":[7],"bioinformatics":[8],"applications":[9],"including":[10],"genome":[11],"assembly,":[12],"sequence":[13,17],"error":[14],"correction,":[15],"and":[16,44,52,58],"alignment.":[18],"As":[19],"the":[20,76,113],"advancements":[21],"next":[23],"generation":[24],"sequencing":[25],"technologies":[26],"have":[27],"resulted":[28],"tremendous":[30],"growth":[31],"of":[32,56,80,96],"genomic":[33],"data,":[34],"it":[35],"inevitable":[37],"for":[38,93,118],"k-mer":[39,115],"counters":[40],"to":[41,69,86,108,112],"be":[42],"faster":[43],"more":[45],"efficient.":[46],"We":[47],"present":[48],"Frigate,":[49],"a":[50],"fast":[51],"efficient":[53],"tool":[54],"capable":[55],"querying":[59],"k-mers.":[60],"Its":[61],"in-memory":[62],"design":[63],"utilizes":[64],"multithreaded,":[65],"lock-free":[66],"data":[67],"structures":[68],"improve":[70],"performance.":[71],"Frigate":[72,103],"was":[73],"developed":[74],"with":[75],"emphasis":[77],"on":[78],"values":[79],"k":[81,97],"less":[82],"than":[83],"20,":[84],"aiming":[85],"maximize":[87],"performance":[88],"by":[89],"employing":[90],"different":[91,94],"algorithms":[92],"ranges":[95],"values.":[98],"The":[99],"results":[100],"show":[101],"that":[102],"achieves":[104],"comparable":[105],"or":[106],"up":[107],"2-3x":[109],"speedup":[110],"compared":[111],"state-of-the-art":[114],"counters,":[116],"especially":[117],"large":[119],"datasets.":[120]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}