{"id":"https://openalex.org/W3189302298","doi":"https://doi.org/10.1109/bhi50953.2021.9508479","title":"KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data","display_name":"KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data","publication_year":2021,"publication_date":"2021-07-27","ids":{"openalex":"https://openalex.org/W3189302298","doi":"https://doi.org/10.1109/bhi50953.2021.9508479","mag":"3189302298","pmid":"https://pubmed.ncbi.nlm.nih.gov/34447942"},"language":"en","primary_location":{"id":"doi:10.1109/bhi50953.2021.9508479","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bhi50953.2021.9508479","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE EMBS International Conference on Biomedical and Health Informatics (BHI)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8383893","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039419132","display_name":"Mattia Prosperi","orcid":"https://orcid.org/0000-0002-9021-5595"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mattia Prosperi","raw_affiliation_strings":["College of Public Health and Health Professions University of Florida,Data Intelligence Systems Lab,Department of Epidemiology,Gainesville,FL,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Public Health and Health Professions University of Florida,Data Intelligence Systems Lab,Department of Epidemiology,Gainesville,FL,USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004394877","display_name":"Simone Marini","orcid":"https://orcid.org/0000-0002-5704-3533"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Simone Marini","raw_affiliation_strings":["College of Public Health and Health Professions University of Florida,Data Intelligence Systems Lab,Department of Epidemiology,Gainesville,FL,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Public Health and Health Professions University of Florida,Data Intelligence Systems Lab,Department of Epidemiology,Gainesville,FL,USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"2021","issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9933000206947327,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9933000206947327,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9801999926567078,"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/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9763000011444092,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/resistome","display_name":"Resistome","score":0.8749390840530396},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7938109636306763},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6762107610702515},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.6572254300117493},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.53908771276474},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.47717538475990295},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.46400633454322815},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4605694115161896},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44508126378059387},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.43274614214897156},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3729078769683838},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.32012081146240234},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29413360357284546},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2725188732147217},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26609426736831665},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23039531707763672},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14163798093795776},{"id":"https://openalex.org/keywords/mobile-genetic-elements","display_name":"Mobile genetic elements","score":0.11422517895698547}],"concepts":[{"id":"https://openalex.org/C2776666601","wikidata":"https://www.wikidata.org/wiki/Q3457855","display_name":"Resistome","level":5,"score":0.8749390840530396},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7938109636306763},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6762107610702515},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.6572254300117493},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.53908771276474},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.47717538475990295},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.46400633454322815},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4605694115161896},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44508126378059387},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.43274614214897156},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3729078769683838},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.32012081146240234},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29413360357284546},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2725188732147217},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26609426736831665},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23039531707763672},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14163798093795776},{"id":"https://openalex.org/C132533263","wikidata":"https://www.wikidata.org/wiki/Q2347362","display_name":"Mobile genetic elements","level":4,"score":0.11422517895698547},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bhi50953.2021.9508479","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bhi50953.2021.9508479","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE EMBS International Conference on Biomedical and Health Informatics (BHI)","raw_type":"proceedings-article"},{"id":"pmid:34447942","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34447942","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-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8383893","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8383893","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE EMBS Int Conf Biomed Health Inform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8383893","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8383893","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE EMBS Int Conf Biomed Health Inform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4098248802","display_name":null,"funder_award_id":"R01 AI141810","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W2008274231","https://openalex.org/W2012365024","https://openalex.org/W2084646638","https://openalex.org/W2133348185","https://openalex.org/W2460324897","https://openalex.org/W2557776122","https://openalex.org/W2606692795","https://openalex.org/W2884944393","https://openalex.org/W2897927784","https://openalex.org/W2898604559","https://openalex.org/W2951274106","https://openalex.org/W2965998894","https://openalex.org/W2968322804","https://openalex.org/W2982531295","https://openalex.org/W2982531601","https://openalex.org/W2983351185","https://openalex.org/W2986916574","https://openalex.org/W3005670610","https://openalex.org/W3015565387","https://openalex.org/W6769556952","https://openalex.org/W6770017517"],"related_works":["https://openalex.org/W4313598112","https://openalex.org/W2097029864","https://openalex.org/W3128872455","https://openalex.org/W2996384775","https://openalex.org/W2078447778","https://openalex.org/W2973098646","https://openalex.org/W2926763004","https://openalex.org/W2789608590","https://openalex.org/W2809850832","https://openalex.org/W3189302298"],"abstract_inverted_index":{"High-throughput":[0],"sequencing":[1,30],"is":[2,51,120,139,181],"widely":[3],"used":[4],"for":[5,75,122,130],"strain":[6],"detection":[7],"and":[8,53,59,99,127,135,157,175],"characterization":[9],"of":[10,108,128],"antibiotic":[11,22,66,116],"resistance":[12,23,68,117],"in":[13],"microbial":[14],"metagenomic":[15,79],"samples.":[16],"Current":[17],"analytical":[18],"tools":[19,167],"use":[20],"curated":[21],"gene":[24,67],"(ARG)":[25],"databases":[26],"to":[27,56],"classify":[28],"individual":[29,101],"reads":[31],"or":[32,49],"assembled":[33],"contigs.":[34],"However,":[35],"identifying":[36,76],"ARGs":[37,77,142],"from":[38,78],"raw":[39],"read":[40,81,102],"data":[41],"can":[42],"be":[43],"time":[44],"consuming":[45],"(especially":[46],"if":[47],"assembly":[48],"alignment":[50],"required)":[52],"challenging,":[54],"due":[55],"genome":[57],"rearrangements":[58],"mutations.":[60],"Here,":[61],"we":[62],"present":[63],"the":[64,109,184],"k-mer-based":[65],"analyzer":[69],"(KARGA),":[70],"a":[71],"multi-platform":[72],"Java":[73],"toolkit":[74],"short":[80],"data.":[82],"KARGA":[83,148,159,180],"does":[84],"not":[85],"perform":[86],"alignment;":[87],"it":[88,138],"uses":[89],"an":[90],"efficient":[91],"double-lookup":[92],"strategy,":[93],"statistical":[94],"filtering":[95],"on":[96,141],"false":[97],"positives,":[98],"provides":[100,149],"classification":[103],"as":[104,106],"well":[105],"covering":[107],"database":[110],"resistome.":[111],"On":[112,145],"simulated":[113],"data,":[114,147],"KARGA\u2019s":[115],"class":[118],"recall":[119],"99.89%":[121],"error/mutation":[123,131],"rates":[124,132],"within":[125],"10%,":[126],"83.37%":[129],"between":[133],"10%":[134],"25%,":[136],"while":[137],"99.92%":[140],"with":[143],"rearrangements.":[144],"empirical":[146],"higher":[150],"hit":[151],"score":[152],"(\u22651.5-fold)":[153],"than":[154,164,170,173,178],"AMRPlusPlus,":[155,171],"DeepARG,":[156,174],"MetaMARC.":[158],"has":[160],"also":[161],"faster":[162,169],"runtimes":[163],"all":[165],"other":[166],"(2x":[168],"7x":[172],"over":[176],"100x":[177],"MetaMARC).":[179],"available":[182],"under":[183],"MIT":[185],"license":[186],"at":[187],"https://github.com/DataIntellSystLab/KARGA.":[188]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
