{"id":"https://openalex.org/W2897603144","doi":"https://doi.org/10.1109/tcbb.2018.2876855","title":"MEC: Misassembly Error Correction in Contigs based on Distribution of Paired-End Reads and Statistics of GC-contents","display_name":"MEC: Misassembly Error Correction in Contigs based on Distribution of Paired-End Reads and Statistics of GC-contents","publication_year":2018,"publication_date":"2018-10-18","ids":{"openalex":"https://openalex.org/W2897603144","doi":"https://doi.org/10.1109/tcbb.2018.2876855","mag":"2897603144","pmid":"https://pubmed.ncbi.nlm.nih.gov/30334805"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2018.2876855","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2876855","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/A5112707856","display_name":"Binbin Wu","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":true,"raw_author_name":"Binbin Wu","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","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, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088826157","display_name":"Xingyu Liao","orcid":"https://orcid.org/0000-0002-0061-1317"},"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":"Xingyu Liao","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, 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/I4210166499","display_name":"Henan Polytechnic University","ror":"https://ror.org/05vr1c885","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210166499"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junwei Luo","raw_affiliation_strings":["College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, China","institution_ids":["https://openalex.org/I4210166499"]}]},{"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, Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, Division of Biomedical 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, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, USA","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, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5112707856"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":null,"apc_paid":null,"fwci":1.0111,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.76110773,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"17","issue":"3","first_page":"847","last_page":"857"},"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.991100013256073,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9753000140190125,"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":0.9634146690368652},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.6600157618522644},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6467611789703369},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.419899046421051},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.40555059909820557},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3995622396469116},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3594025671482086},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21198081970214844},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15930268168449402},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.11254474520683289}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.9634146690368652},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.6600157618522644},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6467611789703369},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.419899046421051},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.40555059909820557},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3995622396469116},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3594025671482086},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21198081970214844},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15930268168449402},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.11254474520683289},{"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0}],"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":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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},{"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:10.1109/tcbb.2018.2876855","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2876855","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:30334805","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30334805","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/G358564744","display_name":null,"funder_award_id":"61420106009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4066238608","display_name":null,"funder_award_id":"B18059","funder_id":"https://openalex.org/F4320327912","funder_display_name":"Higher Education Discipline Innovation Project"},{"id":"https://openalex.org/G8197908271","display_name":null,"funder_award_id":"1053320171177","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"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/F4320327912","display_name":"Higher Education Discipline Innovation Project","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W576031931","https://openalex.org/W1966822396","https://openalex.org/W1970995855","https://openalex.org/W1975398519","https://openalex.org/W1998330439","https://openalex.org/W2004416209","https://openalex.org/W2095841885","https://openalex.org/W2107772251","https://openalex.org/W2111829451","https://openalex.org/W2114765236","https://openalex.org/W2114795390","https://openalex.org/W2115501618","https://openalex.org/W2117383593","https://openalex.org/W2120902911","https://openalex.org/W2121840477","https://openalex.org/W2121911035","https://openalex.org/W2124827052","https://openalex.org/W2126552018","https://openalex.org/W2127768708","https://openalex.org/W2127781493","https://openalex.org/W2129744420","https://openalex.org/W2129933858","https://openalex.org/W2131813051","https://openalex.org/W2135361281","https://openalex.org/W2140059069","https://openalex.org/W2142027180","https://openalex.org/W2142749416","https://openalex.org/W2160053034","https://openalex.org/W2160969485","https://openalex.org/W2166171121","https://openalex.org/W2170551349","https://openalex.org/W2180318265","https://openalex.org/W2330617919","https://openalex.org/W2396849069","https://openalex.org/W2520464109","https://openalex.org/W2607811538","https://openalex.org/W2610924493","https://openalex.org/W2782397389","https://openalex.org/W2886623299","https://openalex.org/W2890720538","https://openalex.org/W2905576637","https://openalex.org/W6754330492"],"related_works":["https://openalex.org/W2089480001","https://openalex.org/W2885619582","https://openalex.org/W3167837387","https://openalex.org/W54719527","https://openalex.org/W4250462852","https://openalex.org/W2060480089","https://openalex.org/W2944010518","https://openalex.org/W1992950355","https://openalex.org/W4381279187","https://openalex.org/W2013063066"],"abstract_inverted_index":{"The":[0],"de":[1],"novo":[2],"assembly":[3,16,48],"tools":[4,17],"aim":[5],"at":[6,153],"reconstructing":[7],"genomes":[8],"from":[9],"next-generation":[10],"sequencing":[11,39],"(NGS)":[12],"data.":[13],"However,":[14],"the":[15,45,53,80,88,104,114,126],"usually":[18],"generate":[19],"a":[20,64],"large":[21],"amount":[22],"of":[23,33,47,84,91,128],"contigs":[24,56],"containing":[25],"many":[26],"misassemblies,":[27],"which":[28,133],"are":[29,57],"caused":[30],"by":[31],"problems":[32],"repetitive":[34],"regions,":[35],"chimeric":[36],"reads,":[37],"and":[38,51,73,87,120,141],"errors.":[40],"As":[41],"they":[42],"can":[43,94,137],"improve":[44],"accuracy":[46],"results,":[49,132],"detecting":[50],"correcting":[52],"misassemblies":[54,75,97,139],"in":[55,76,143,146],"appealing,":[58],"yet":[59],"challenging.":[60],"In":[61],"this":[62],"study,":[63],"novel":[65],"method,":[66],"called":[67],"MEC,":[68],"is":[69,150],"proposed":[70],"to":[71,124],"identify":[72,95],"correct":[74],"contigs.":[77],"Based":[78],"on":[79,108,130],"insert":[81],"size":[82],"distribution":[83],"paired-end":[85],"reads":[86],"statistical":[89],"analysis":[90],"GC-contents,":[92],"MEC":[93,102,129,136,149],"more":[96],"accurately.":[98],"We":[99],"evaluate":[100],"our":[101],"with":[103,113],"metrics":[105],"(NA50,":[106],"NGA50)":[107],"four":[109],"datasets,":[110],"compared":[111],"it":[112],"most":[115],"available":[116,152],"misassembly":[117],"correction":[118],"tools,":[119],"carry":[121],"out":[122],"experiments":[123],"analyze":[125],"influence":[127],"scaffolding":[131,147],"shows":[134],"that":[135],"reduce":[138],"effectively":[140],"result":[142],"quantitative":[144],"improvements":[145],"quality.":[148],"publicly":[151],"https://github.com/bioinfomaticsCSU/MEC.":[154]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":6}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}