{"id":"https://openalex.org/W2167469524","doi":"https://doi.org/10.1093/bioinformatics/btv415","title":"Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data","display_name":"Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data","publication_year":2015,"publication_date":"2015-07-14","ids":{"openalex":"https://openalex.org/W2167469524","doi":"https://doi.org/10.1093/bioinformatics/btv415","mag":"2167469524"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv415","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv415","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/21/3421/17122504/btv415.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/21/3421/17122504/btv415.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037145360","display_name":"Amin Allam","orcid":"https://orcid.org/0000-0001-5137-0990"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Amin Allam","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014399734","display_name":"Panos Kalnis","orcid":"https://orcid.org/0000-0002-5060-1360"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Panos Kalnis","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019821677","display_name":"Victor Solovyev","orcid":"https://orcid.org/0000-0001-8885-493X"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Victor Solovyev","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5037145360"],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.6138,"has_fulltext":true,"cited_by_count":113,"citation_normalized_percentile":{"value":0.93615563,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"31","issue":"21","first_page":"3421","last_page":"3428"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9825000166893005,"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":0.9657999873161316,"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":0.6947277784347534},{"id":"https://openalex.org/keywords/error-detection-and-correction","display_name":"Error detection and correction","score":0.6874701976776123},{"id":"https://openalex.org/keywords/substitution","display_name":"Substitution (logic)","score":0.6392072439193726},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5001380443572998},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.46430283784866333},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4206398129463196},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41500604152679443},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4078153669834137},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21739479899406433},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18964418768882751},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13024109601974487}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6947277784347534},{"id":"https://openalex.org/C103088060","wikidata":"https://www.wikidata.org/wiki/Q1062839","display_name":"Error detection and correction","level":2,"score":0.6874701976776123},{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.6392072439193726},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5001380443572998},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.46430283784866333},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4206398129463196},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41500604152679443},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4078153669834137},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21739479899406433},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18964418768882751},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13024109601974487},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv415","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv415","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/21/3421/17122504/btv415.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/21/3421","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/21/3421","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:repository.kaust.edu.sa:10754/567063","is_oa":false,"landing_page_url":"http://hdl.handle.net/10754/567063","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah 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/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv415","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv415","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/21/3421/17122504/btv415.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167469524.pdf","grobid_xml":"https://content.openalex.org/works/W2167469524.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1912338927","https://openalex.org/W1980032728","https://openalex.org/W1980667059","https://openalex.org/W1983403167","https://openalex.org/W2001079689","https://openalex.org/W2009735916","https://openalex.org/W2010044484","https://openalex.org/W2014099509","https://openalex.org/W2022986961","https://openalex.org/W2041126213","https://openalex.org/W2049511729","https://openalex.org/W2074231493","https://openalex.org/W2075013491","https://openalex.org/W2084734290","https://openalex.org/W2096634299","https://openalex.org/W2101250487","https://openalex.org/W2107772251","https://openalex.org/W2113154626","https://openalex.org/W2115501618","https://openalex.org/W2117945751","https://openalex.org/W2119745866","https://openalex.org/W2120902911","https://openalex.org/W2121530737","https://openalex.org/W2122812051","https://openalex.org/W2127768708","https://openalex.org/W2129276621","https://openalex.org/W2131776122","https://openalex.org/W2133956160","https://openalex.org/W2136651963","https://openalex.org/W2139306346","https://openalex.org/W2142113273","https://openalex.org/W2142702487","https://openalex.org/W2144993653","https://openalex.org/W2152246890","https://openalex.org/W2155845142","https://openalex.org/W2157888653","https://openalex.org/W2160177274","https://openalex.org/W2160265768","https://openalex.org/W2160665949","https://openalex.org/W2160770624","https://openalex.org/W2160969485","https://openalex.org/W2161546116","https://openalex.org/W2167699390","https://openalex.org/W2168602018","https://openalex.org/W2399217527","https://openalex.org/W2523692606","https://openalex.org/W6639925919","https://openalex.org/W6679676508","https://openalex.org/W6712655656"],"related_works":["https://openalex.org/W2166395958","https://openalex.org/W1483251870","https://openalex.org/W2128684264","https://openalex.org/W2016966302","https://openalex.org/W2159998739","https://openalex.org/W2593809815","https://openalex.org/W2039079849","https://openalex.org/W2255506873","https://openalex.org/W4378801540","https://openalex.org/W4280563294"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Next-generation":[2],"sequencing":[3,100],"generates":[4],"large":[5],"amounts":[6],"of":[7,15,20,86,114,147],"data":[8,92,163],"affected":[9],"by":[10],"errors":[11,40,117],"in":[12,49,112,122,135],"the":[13,26,87,145],"form":[14],"substitutions,":[16],"insertions":[17,44],"or":[18],"deletions":[19],"bases.":[21],"Error":[22],"correction":[23,61],"based":[24,63],"on":[25,64],"high-coverage":[27],"information,":[28],"typically":[29],"improves":[30],"de":[31,127],"novo":[32,128],"assembly.":[33],"Most":[34],"existing":[35],"tools":[36],"can":[37,76],"correct":[38],"substitution":[39],"only;":[41],"some":[42],"support":[43],"and":[45,72,97,125,151],"deletions,":[46],"but":[47],"accuracy":[48,123],"many":[50],"cases":[51],"is":[52,105,154],"low.":[53],"Results:":[54],"We":[55,137],"present":[56],"Karect,":[57],"a":[58],"novel":[59],"error":[60,148],"technique":[62],"multiple":[65],"alignment.":[66],"Our":[67],"approach":[68],"supports":[69],"substitution,":[70],"insertion":[71],"deletion":[73],"errors.":[74],"It":[75],"handle":[77],"non-uniform":[78],"coverage":[79],"as":[80,82],"well":[81],"moderately":[83],"covered":[84],"areas":[85],"sequenced":[88],"genome.":[89],"Experiments":[90],"with":[91],"from":[93],"Illumina,":[94],"454":[95],"FLX":[96],"Ion":[98],"Torrent":[99],"machines":[101],"demonstrate":[102],"that":[103],"Karect":[104,153],"more":[106],"accurate":[107],"than":[108],"previous":[109],"methods,":[110],"both":[111],"terms":[113],"correcting":[115],"individual-bases":[116],"(up":[118,131],"to":[119,132],"10%":[120,133],"increase":[121,134],"gain)":[124],"post":[126],"assembly":[129],"quality":[130,146],"NGA50).":[136],"also":[138],"introduce":[139],"an":[140],"improved":[141],"framework":[142],"for":[143],"evaluating":[144],"correction.":[149],"Availability":[150],"implementation:":[152],"available":[155,165],"at:":[156],"http://aminallam.github.io/karect.":[157],"Contact:":[158],"amin.allam@kaust.edu.sa":[159],"Supplementary":[160,162],"information:":[161],"are":[164],"at":[166],"Bioinformatics":[167],"online.":[168]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":8},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2016-06-24T00:00:00"}