{"id":"https://openalex.org/W2883056464","doi":"https://doi.org/10.1109/tcbb.2018.2858267","title":"A Novel Scaffolding Algorithm Based on Contig Error Correction and Path Extension","display_name":"A Novel Scaffolding Algorithm Based on Contig Error Correction and Path Extension","publication_year":2018,"publication_date":"2018-07-20","ids":{"openalex":"https://openalex.org/W2883056464","doi":"https://doi.org/10.1109/tcbb.2018.2858267","mag":"2883056464","pmid":"https://pubmed.ncbi.nlm.nih.gov/30040649"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2018.2858267","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2858267","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"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":"Min Li","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, P. R. China"],"raw_orcid":"https://orcid.org/0000-0002-0188-1394","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, P. R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103788844","display_name":"Li Tang","orcid":null},"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":"Li Tang","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, P. R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044853928","display_name":"Zhongxiang Liao","orcid":null},"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":"Zhongxiang Liao","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, P. R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100422484","display_name":"Junwei Luo","orcid":"https://orcid.org/0000-0001-6841-9893"},"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":"Junwei Luo","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, P. R. China"],"raw_orcid":"https://orcid.org/0000-0001-6841-9893","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, P. R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091157395","display_name":"Fang\u2010Xiang Wu","orcid":"https://orcid.org/0000-0002-4593-9332"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Fang-Xiang Wu","raw_affiliation_strings":["Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Canada"],"raw_orcid":"https://orcid.org/0000-0002-4593-9332","affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101465265","display_name":"Yi Pan","orcid":"https://orcid.org/0000-0002-2766-3096"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi Pan","raw_affiliation_strings":["Department of Computer Science, Georgia State University, Atlanta, GA"],"raw_orcid":"https://orcid.org/0000-0002-2766-3096","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA","institution_ids":["https://openalex.org/I181565077"]}]},{"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":false,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, P. R. China"],"raw_orcid":"https://orcid.org/0000-0003-1516-0480","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, P. R. China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6315,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.67459254,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"16","issue":"3","first_page":"764","last_page":"773"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.994700014591217,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.965499997138977,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.8921536207199097},{"id":"https://openalex.org/keywords/correctness","display_name":"Correctness","score":0.875967264175415},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.7291645407676697},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.634039580821991},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5941796898841858},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5498148202896118},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.544901430606842},{"id":"https://openalex.org/keywords/scaffold","display_name":"Scaffold","score":0.49724796414375305},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.48445940017700195},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.13415458798408508},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09118238091468811},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.085669606924057}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.8921536207199097},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.875967264175415},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.7291645407676697},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.634039580821991},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5941796898841858},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5498148202896118},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.544901430606842},{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.49724796414375305},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.48445940017700195},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.13415458798408508},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09118238091468811},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.085669606924057},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2018.2858267","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2858267","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30040649","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30040649","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/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1187543282","display_name":null,"funder_award_id":"61772557","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1729077721","display_name":null,"funder_award_id":"61732009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7076079901","display_name":null,"funder_award_id":"2017zzts714","funder_id":"https://openalex.org/F4320321514","funder_display_name":"Central South University"},{"id":"https://openalex.org/G8210156615","display_name":null,"funder_award_id":"61622213","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/F4320321514","display_name":"Central South University","ror":"https://ror.org/00f1zfq44"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":64,"referenced_works":["https://openalex.org/W576031931","https://openalex.org/W1903088142","https://openalex.org/W1966822396","https://openalex.org/W1970995855","https://openalex.org/W1972924519","https://openalex.org/W1975398519","https://openalex.org/W1990601349","https://openalex.org/W1995663053","https://openalex.org/W2041391522","https://openalex.org/W2046137036","https://openalex.org/W2063399687","https://openalex.org/W2076151007","https://openalex.org/W2083215220","https://openalex.org/W2094397139","https://openalex.org/W2097341408","https://openalex.org/W2103441770","https://openalex.org/W2103903744","https://openalex.org/W2105067980","https://openalex.org/W2105368763","https://openalex.org/W2107164256","https://openalex.org/W2108234281","https://openalex.org/W2108640362","https://openalex.org/W2111829451","https://openalex.org/W2112113834","https://openalex.org/W2114795390","https://openalex.org/W2115501618","https://openalex.org/W2115920539","https://openalex.org/W2119180969","https://openalex.org/W2120048439","https://openalex.org/W2121832832","https://openalex.org/W2124827052","https://openalex.org/W2124960286","https://openalex.org/W2124985265","https://openalex.org/W2126057141","https://openalex.org/W2126552018","https://openalex.org/W2128114769","https://openalex.org/W2129744420","https://openalex.org/W2130347047","https://openalex.org/W2139760555","https://openalex.org/W2140059069","https://openalex.org/W2142027180","https://openalex.org/W2145186656","https://openalex.org/W2152073175","https://openalex.org/W2154503441","https://openalex.org/W2155004936","https://openalex.org/W2157624015","https://openalex.org/W2161724277","https://openalex.org/W2165795500","https://openalex.org/W2166501262","https://openalex.org/W2169002484","https://openalex.org/W2170551349","https://openalex.org/W2171531867","https://openalex.org/W2288105190","https://openalex.org/W2291614554","https://openalex.org/W2323851578","https://openalex.org/W2330617919","https://openalex.org/W2520464109","https://openalex.org/W2578045105","https://openalex.org/W2610924493","https://openalex.org/W2739107670","https://openalex.org/W2753031018","https://openalex.org/W2766029068","https://openalex.org/W2905576637","https://openalex.org/W3019065848"],"related_works":["https://openalex.org/W1994449010","https://openalex.org/W1667647204","https://openalex.org/W2404647514","https://openalex.org/W4247536566","https://openalex.org/W2074936491","https://openalex.org/W2069489638","https://openalex.org/W2018477250","https://openalex.org/W3119814709","https://openalex.org/W4241418540","https://openalex.org/W1508895727"],"abstract_inverted_index":{"The":[0,16,61],"sequence":[1,31],"assembly":[2],"process":[3,25],"can":[4,65,148],"be":[5,66],"divided":[6],"into":[7],"three":[8],"stages:":[9],"contigs":[10],"extension,":[11],"scaffolding,":[12],"and":[13,30,49,92,106,131,161,176],"gap":[14,152],"filling.":[15],"scaffolding":[17,37,64,80,182],"method":[18],"is":[19,83,141,168],"an":[20],"essential":[21],"step":[22],"during":[23],"the":[24,28,34,40,85,101,108,120,126,135,138,143,151,162,172],"to":[26,55,133,170],"infer":[27],"direction":[29],"relationships":[32,58,103],"between":[33,59,73,104],"contigs.":[35,60,74],"However,":[36],"still":[38],"faces":[39],"challenges":[41],"of":[42,63,87,110,122,128,174],"uneven":[43],"sequencing":[44,50],"depth,":[45],"genome":[46],"repetitive":[47],"regions,":[48],"errors,":[51],"which":[52,82,118,140],"often":[53],"leads":[54],"many":[56],"false":[57,71,102],"performance":[62],"improved":[67],"by":[68,125],"removing":[69],"potential":[70],"conjunctions":[72],"In":[75],"this":[76],"study,":[77],"a":[78,115],"novel":[79],"algorithm":[81],"on":[84,157],"basis":[86],"path":[88,139],"extension":[89,136],"Loose-Strict-Loose":[90],"strategy":[91,167],"contig":[93],"error":[94],"correction,":[95],"called":[96],"iLSLS.":[97],"iLSLS":[98,113,147,177],"helps":[99],"reduce":[100],"contigs,":[105],"improve":[107],"accuracy":[109],"subsequent":[111],"steps.":[112],"utilizes":[114],"scoring":[116],"function,":[117],"estimates":[119],"correctness":[121,173],"candidate":[123],"paths":[124],"distribution":[127],"paired":[129],"reads,":[130],"try":[132],"conduction":[134],"with":[137],"scored":[142],"highest.":[144],"What's":[145],"more,":[146],"precisely":[149],"estimate":[150],"size.":[153],"We":[154],"conduct":[155],"experiments":[156],"two":[158],"real":[159],"datasets,":[160],"results":[163],"show":[164],"that":[165],"LSLS":[166],"efficient":[169],"increase":[171],"scaffolds,":[175],"performs":[178],"better":[179],"than":[180],"other":[181],"methods.":[183]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
