{"id":"https://openalex.org/W4292255094","doi":"https://doi.org/10.1093/bioinformatics/btac565","title":"Fec: a fast error correction method based on two-rounds overlapping and caching","display_name":"Fec: a fast error correction method based on two-rounds overlapping and caching","publication_year":2022,"publication_date":"2022-08-17","ids":{"openalex":"https://openalex.org/W4292255094","doi":"https://doi.org/10.1093/bioinformatics/btac565","pmid":"https://pubmed.ncbi.nlm.nih.gov/35977383"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac565","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac565","pdf_url":null,"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","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/A5100433167","display_name":"Jun Zhang","orcid":"https://orcid.org/0000-0002-5222-1898"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Zhang","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha 410083, China","School of Computer Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025266142","display_name":"Fan Nie","orcid":"https://orcid.org/0000-0003-1013-5235"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fan Nie","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha 410083, China","School of Computer Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054096088","display_name":"Neng Huang","orcid":"https://orcid.org/0000-0001-7187-0749"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Neng Huang","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha 410083, China","School of Computer Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090322041","display_name":"Peng Ni","orcid":"https://orcid.org/0000-0002-0801-7574"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peng Ni","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha 410083, China","School of Computer Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100683466","display_name":"Feng Luo","orcid":"https://orcid.org/0000-0002-4813-2403"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Feng Luo","raw_affiliation_strings":["School of Computing, Clemson University , Clemson, SC 29634, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, Clemson University , Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":"https://orcid.org/0000-0003-1516-0480"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha 410083, China","School of Computer Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":"https://orcid.org/0000-0003-1516-0480","affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100438360"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08155483,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"38","issue":"19","first_page":"4629","last_page":"4632"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.994700014591217,"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":0.994700014591217,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.0007999999797903001,"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"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/computer-science","display_name":"Computer science","score":0.7472506761550903},{"id":"https://openalex.org/keywords/error-detection-and-correction","display_name":"Error detection and correction","score":0.5202766060829163},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.42257818579673767}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7472506761550903},{"id":"https://openalex.org/C103088060","wikidata":"https://www.wikidata.org/wiki/Q1062839","display_name":"Error detection and correction","level":2,"score":0.5202766060829163},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42257818579673767}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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:10.1093/bioinformatics/btac565","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac565","pdf_url":null,"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":"pmid:35977383","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35977383","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1279979837","display_name":null,"funder_award_id":"62150048","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G611205877","display_name":null,"funder_award_id":"2021YFF1201200","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8196091623","display_name":null,"funder_award_id":"U1909208","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1579534339","https://openalex.org/W1983403167","https://openalex.org/W2141978199","https://openalex.org/W2157888653","https://openalex.org/W2160177274","https://openalex.org/W2340761128","https://openalex.org/W2346241034","https://openalex.org/W2604588349","https://openalex.org/W2755804176","https://openalex.org/W2788228074","https://openalex.org/W2789843538","https://openalex.org/W2808352813","https://openalex.org/W2950354111","https://openalex.org/W3120530641"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829"],"abstract_inverted_index":{"The":[0],"third-generation":[1],"sequencing":[2,32],"technology":[3],"has":[4,221],"advanced":[5],"genome":[6],"analysis":[7],"with":[8,162],"long-read":[9],"length,":[10],"but":[11],"the":[12,19,31,46,61,76,84,123,142,145,160,166,175,179,183,192,204,207,216],"reads":[13,42,161],"need":[14],"error":[15,21,48,98,115],"correction":[16,24,49,99,116],"due":[17],"to":[18,57,70,133,138,155,226,240],"high":[20],"rate.":[22],"Error":[23],"is":[25,34,72,153,252],"a":[26,38,52,96,128,148],"time-consuming":[27],"process":[28],"especially":[29],"when":[30,59,74],"coverage":[33],"high.":[35],"Generally,":[36],"for":[37,159],"pair":[39],"of":[40,141],"overlapping":[41,104],"A":[43,58,69],"and":[44,105,190,202,215,229,235,242],"B,":[45],"existing":[47],"methods":[50],"perform":[51],"base-level":[53,66,85,171,200],"alignment":[54,67,86,180,188,194,201,205],"from":[55,68,195],"B":[56,71],"correcting":[60,75],"read":[62,77],"A.":[63],"And":[64],"another":[65],"performed":[73],"B.":[78],"However,":[79],"based":[80],"on":[81,212,231,244],"our":[82],"observation,":[83],"information":[87],"can":[88,108],"be":[89,109],"reused.":[90],"In":[91,122,144],"this":[92,187],"article,":[93],"we":[94],"present":[95],"fast":[97],"tool":[100],"Fec,":[101],"using":[102],"two-rounds":[103],"caching.":[106],"Fec":[107,126,173,185,198,211,220,251],"used":[110,154],"independently":[111],"or":[112],"as":[113],"an":[114,119],"step":[117],"in":[118,165,182,206],"assembly":[120],"pipeline.":[121],"first":[124,167],"round,":[125,147],"uses":[127],"large":[129],"window":[130,150],"size":[131,151],"(20)":[132],"quickly":[134],"find":[135,156],"enough":[136],"overlaps":[137,158,164],"correct":[139],"most":[140],"reads.":[143],"second":[146,193],"small":[149],"(5)":[152],"more":[157],"insufficient":[163],"round.":[168],"When":[169],"performing":[170],"alignment,":[172],"searches":[174],"cache":[176],"first.":[177],"If":[178],"exists":[181],"cache,":[184],"takes":[186],"out":[189],"deduces":[191],"it.":[196],"Otherwise,":[197],"performs":[199],"stores":[203],"cache.":[208],"We":[209],"test":[210],"nine":[213],"datasets,":[214],"results":[217],"show":[218],"that":[219],"1.24-38.56":[222],"times":[223,237],"speed-up":[224,238],"compared":[225,239],"MECAT,":[227],"CANU":[228,243],"MINICNS":[230],"five":[232],"PacBio":[233],"datasets":[234],"1.16-27.8":[236],"NECAT":[241],"four":[245],"nanopore":[246],"datasets.":[247],"AVAILABILITY":[248],"AND":[249],"IMPLEMENTATION:":[250],"available":[253,261],"at":[254,262],"https://github.com/zhangjuncsu/Fec.":[255],"SUPPLEMENTARY":[256],"INFORMATION:":[257],"Supplementary":[258],"data":[259],"are":[260],"Bioinformatics":[263],"online.":[264]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
