{"id":"https://openalex.org/W2766504919","doi":"https://doi.org/10.1093/bib/bbx147","title":"Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data","display_name":"Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data","publication_year":2017,"publication_date":"2017-10-19","ids":{"openalex":"https://openalex.org/W2766504919","doi":"https://doi.org/10.1093/bib/bbx147","mag":"2766504919","pmid":"https://pubmed.ncbi.nlm.nih.gov/29112696"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbx147","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbx147","pdf_url":"https://academic.oup.com/bib/article-pdf/20/3/866/28847287/bbx147.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/20/3/866/28847287/bbx147.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026034483","display_name":"Vasanthan Jayakumar","orcid":"https://orcid.org/0000-0002-6067-4184"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Vasanthan Jayakumar","raw_affiliation_strings":["Department of Biosciences and Informatics, Keio University, Japan"],"raw_orcid":"https://orcid.org/0000-0002-6067-4184","affiliations":[{"raw_affiliation_string":"Department of Biosciences and Informatics, Keio University, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025573915","display_name":"Yasubumi Sakakibara","orcid":"https://orcid.org/0000-0002-6932-3452"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yasubumi Sakakibara","raw_affiliation_strings":["Department of Biosciences and Informatics, Keio University, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Informatics, Keio University, Japan","institution_ids":["https://openalex.org/I203951103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5025573915"],"corresponding_institution_ids":["https://openalex.org/I203951103"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.492,"has_fulltext":true,"cited_by_count":118,"citation_normalized_percentile":{"value":0.95624122,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"20","issue":"3","first_page":"866","last_page":"876"},"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/T11470","display_name":"Legume Nitrogen Fixing Symbiosis","score":0.9681000113487244,"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/T11879","display_name":"Protist diversity and phylogeny","score":0.9643999934196472,"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/sequence-assembly","display_name":"Sequence assembly","score":0.7431277632713318},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6388130187988281},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6386438012123108},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5573246479034424},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5402803421020508},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4100549817085266},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2058466374874115},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18576335906982422}],"concepts":[{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.7431277632713318},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6388130187988281},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6386438012123108},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5573246479034424},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5402803421020508},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4100549817085266},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2058466374874115},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18576335906982422},{"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":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D027741","descriptor_name":"Ipomoea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027741","descriptor_name":"Ipomoea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027741","descriptor_name":"Ipomoea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027741","descriptor_name":"Ipomoea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbx147","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbx147","pdf_url":"https://academic.oup.com/bib/article-pdf/20/3/866/28847287/bbx147.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29112696","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29112696","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:6585154","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6585154","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbx147","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbx147","pdf_url":"https://academic.oup.com/bib/article-pdf/20/3/866/28847287/bbx147.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3361386922","display_name":null,"funder_award_id":"16H06279","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2766504919.pdf","grobid_xml":"https://content.openalex.org/works/W2766504919.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W344138311","https://openalex.org/W1579534339","https://openalex.org/W1635391495","https://openalex.org/W1791377616","https://openalex.org/W1957444659","https://openalex.org/W1983403167","https://openalex.org/W2017666255","https://openalex.org/W2101786683","https://openalex.org/W2102532874","https://openalex.org/W2107282968","https://openalex.org/W2107772251","https://openalex.org/W2108640362","https://openalex.org/W2112814753","https://openalex.org/W2127768708","https://openalex.org/W2127781493","https://openalex.org/W2129003604","https://openalex.org/W2135361281","https://openalex.org/W2137759177","https://openalex.org/W2144560237","https://openalex.org/W2155628349","https://openalex.org/W2157888653","https://openalex.org/W2161901637","https://openalex.org/W2169773990","https://openalex.org/W2194172909","https://openalex.org/W2202810729","https://openalex.org/W2211504288","https://openalex.org/W2323608404","https://openalex.org/W2337513885","https://openalex.org/W2341858319","https://openalex.org/W2346756609","https://openalex.org/W2422772473","https://openalex.org/W2464063823","https://openalex.org/W2468861611","https://openalex.org/W2473686027","https://openalex.org/W2479687279","https://openalex.org/W2485161901","https://openalex.org/W2507370192","https://openalex.org/W2513582464","https://openalex.org/W2538143681","https://openalex.org/W2549065004","https://openalex.org/W2560604625","https://openalex.org/W2562683361","https://openalex.org/W2566610827","https://openalex.org/W2573925251","https://openalex.org/W2575750030","https://openalex.org/W2583479769","https://openalex.org/W2585284430","https://openalex.org/W2594081754","https://openalex.org/W2602637791","https://openalex.org/W2607669908","https://openalex.org/W2608588163","https://openalex.org/W2611605679","https://openalex.org/W2614769193","https://openalex.org/W2623168030","https://openalex.org/W2747802896","https://openalex.org/W2755804176","https://openalex.org/W2763726643","https://openalex.org/W2949097965","https://openalex.org/W2950354111","https://openalex.org/W2950576163","https://openalex.org/W2951803187","https://openalex.org/W2953039206","https://openalex.org/W2953147862","https://openalex.org/W6703514187","https://openalex.org/W6719946149","https://openalex.org/W6725837728","https://openalex.org/W6736678799","https://openalex.org/W7075604223"],"related_works":["https://openalex.org/W2794386548","https://openalex.org/W4381279187","https://openalex.org/W1992950355","https://openalex.org/W2013063066","https://openalex.org/W2890379969","https://openalex.org/W1841715584","https://openalex.org/W2766401759","https://openalex.org/W3215016332","https://openalex.org/W3134563641","https://openalex.org/W1491924329"],"abstract_inverted_index":{"Long":[0],"reads":[1],"obtained":[2],"from":[3,87],"third-generation":[4],"sequencing":[5,53],"platforms":[6],"can":[7,111],"help":[8],"overcome":[9],"the":[10,14,21,42,61,104,132],"long-standing":[11],"challenge":[12],"of":[13,18,24,41,79,135],"de":[15,30],"novo":[16,31],"assembly":[17,117],"sequences":[19],"for":[20,64,129],"genomic":[22,127],"analysis":[23],"non-model":[25,136],"eukaryotic":[26,116],"organisms.":[27,137],"Numerous":[28],"long-read-aided":[29],"assemblies":[32,56,134],"have":[33],"been":[34],"published":[35],"recently,":[36],"which":[37],"exhibited":[38],"superior":[39],"quality":[40],"assembled":[43],"genomes":[44],"in":[45,59,94],"comparison":[46],"with":[47,91],"those":[48],"achieved":[49],"using":[50,76],"earlier":[51],"second-generation":[52],"technologies.":[54],"Evaluating":[55],"is":[57],"important":[58],"guiding":[60],"appropriate":[62],"choice":[63],"specific":[65],"research":[66],"needs.":[67],"In":[68],"this":[69],"study,":[70],"we":[71,120],"evaluated":[72],"10":[73],"long-read":[74],"assemblers":[75,109],"a":[77,107],"variety":[78],"metrics":[80],"on":[81],"Pacific":[82],"Biosciences":[83],"(PacBio)":[84],"data":[85],"sets":[86],"different":[88],"taxonomic":[89],"categories":[90],"considerable":[92],"differences":[93],"genome":[95,133],"size.":[96],"The":[97],"results":[98],"allowed":[99],"us":[100],"to":[101,106,115,124],"narrow":[102],"down":[103],"list":[105],"few":[108],"that":[110],"be":[112],"effectively":[113,130],"applied":[114],"projects.":[118],"Moreover,":[119],"highlight":[121],"how":[122],"best":[123],"use":[125],"limited":[126],"resources":[128],"evaluating":[131]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":14},{"year":2018,"cited_by_count":5},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}