{"id":"https://openalex.org/W3139503429","doi":"https://doi.org/10.1186/s12859-021-04081-z","title":"SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme","display_name":"SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme","publication_year":2021,"publication_date":"2021-03-25","ids":{"openalex":"https://openalex.org/W3139503429","doi":"https://doi.org/10.1186/s12859-021-04081-z","mag":"3139503429","pmid":"https://pubmed.ncbi.nlm.nih.gov/33765921"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04081-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04081-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04081-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04081-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102924223","display_name":"Lidong Guo","orcid":"https://orcid.org/0000-0003-2520-4416"},"institutions":[{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lidong Guo","raw_affiliation_strings":["BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China","BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China","State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043281019","display_name":"Mengyang Xu","orcid":"https://orcid.org/0000-0002-4487-7088"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4210149137","display_name":"China National GeneBank","ror":"https://ror.org/03n9hr695","country_code":"CN","type":"archive","lineage":["https://openalex.org/I4210149137"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengyang Xu","raw_affiliation_strings":["BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China","BGI-Shenzhen, Shenzhen, 518083, China","China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China","State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":"https://orcid.org/0000-0002-4487-7088","affiliations":[{"raw_affiliation_string":"BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China","institution_ids":[]},{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China","institution_ids":["https://openalex.org/I4210149137"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100417820","display_name":"Wenchao Wang","orcid":"https://orcid.org/0000-0003-0757-4878"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wenchao Wang","raw_affiliation_strings":["BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025851429","display_name":"Shengqiang Gu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shengqiang Gu","raw_affiliation_strings":["BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101185116","display_name":"Xia Zhao","orcid":"https://orcid.org/0000-0002-1755-6334"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xia Zhao","raw_affiliation_strings":["MGI, BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MGI, BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007909708","display_name":"Fang Chen","orcid":"https://orcid.org/0000-0002-0242-331X"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fang Chen","raw_affiliation_strings":["MGI, BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MGI, BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101846522","display_name":"Ou Wang","orcid":"https://orcid.org/0000-0001-8673-6497"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4210149137","display_name":"China National GeneBank","ror":"https://ror.org/03n9hr695","country_code":"CN","type":"archive","lineage":["https://openalex.org/I4210149137"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ou Wang","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, 518083, China","China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China","institution_ids":["https://openalex.org/I4210149137"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100451926","display_name":"Xun Xu","orcid":"https://orcid.org/0000-0002-5338-5173"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4210149137","display_name":"China National GeneBank","ror":"https://ror.org/03n9hr695","country_code":"CN","type":"archive","lineage":["https://openalex.org/I4210149137"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xun Xu","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, 518083, China","China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China","institution_ids":["https://openalex.org/I4210149137"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013717991","display_name":"Inge Seim","orcid":"https://orcid.org/0000-0001-8594-7217"},"institutions":[{"id":"https://openalex.org/I152031979","display_name":"Nanjing Normal University","ror":"https://ror.org/036trcv74","country_code":"CN","type":"education","lineage":["https://openalex.org/I152031979"]},{"id":"https://openalex.org/I160993911","display_name":"Queensland University of Technology","ror":"https://ror.org/03pnv4752","country_code":"AU","type":"education","lineage":["https://openalex.org/I160993911"]}],"countries":["AU","CN"],"is_corresponding":false,"raw_author_name":"Inge Seim","raw_affiliation_strings":["Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China","School of Biology and Environmental Science, Queensland University of Technology, Brisbane, 4000, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China","institution_ids":["https://openalex.org/I152031979"]},{"raw_affiliation_string":"School of Biology and Environmental Science, Queensland University of Technology, Brisbane, 4000, Australia","institution_ids":["https://openalex.org/I160993911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056684485","display_name":"Guangyi Fan","orcid":"https://orcid.org/0000-0001-7365-1590"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4210149137","display_name":"China National GeneBank","ror":"https://ror.org/03n9hr695","country_code":"CN","type":"archive","lineage":["https://openalex.org/I4210149137"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guangyi Fan","raw_affiliation_strings":["BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China","BGI-Shenzhen, Shenzhen, 518083, China","China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China","State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":"https://orcid.org/0000-0001-7365-1590","affiliations":[{"raw_affiliation_string":"BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China","institution_ids":[]},{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China","institution_ids":["https://openalex.org/I4210149137"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035008543","display_name":"Li Deng","orcid":"https://orcid.org/0000-0001-8622-1725"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4210088191","display_name":"Agricultural Genomics Institute at Shenzhen","ror":"https://ror.org/0066zpp98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210088191","https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]},{"id":"https://openalex.org/I4210149137","display_name":"China National GeneBank","ror":"https://ror.org/03n9hr695","country_code":"CN","type":"archive","lineage":["https://openalex.org/I4210149137"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Li Deng","raw_affiliation_strings":["BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. dengli1@genomics.cn","BGI-Shenzhen, Shenzhen, 518083, China. dengli1@genomics.cn","China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. dengli1@genomics.cn","State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. dengli1@genomics.cn","State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. dengli1@genomics.cn","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China. dengli1@genomics.cn","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. dengli1@genomics.cn","institution_ids":["https://openalex.org/I4210149137"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. dengli1@genomics.cn","institution_ids":["https://openalex.org/I100135526","https://openalex.org/I4210088191"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100352324","display_name":"Xin Liu","orcid":"https://orcid.org/0000-0003-3256-2940"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4210088191","display_name":"Agricultural Genomics Institute at Shenzhen","ror":"https://ror.org/0066zpp98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210088191","https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]},{"id":"https://openalex.org/I4210149137","display_name":"China National GeneBank","ror":"https://ror.org/03n9hr695","country_code":"CN","type":"archive","lineage":["https://openalex.org/I4210149137"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xin Liu","raw_affiliation_strings":["BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. liuxin@genomics.cn","BGI-Shenzhen, Shenzhen, 518083, China. liuxin@genomics.cn","China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. liuxin@genomics.cn","State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. liuxin@genomics.cn","State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. liuxin@genomics.cn","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China. liuxin@genomics.cn","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. liuxin@genomics.cn","institution_ids":["https://openalex.org/I4210149137"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. liuxin@genomics.cn","institution_ids":["https://openalex.org/I100135526","https://openalex.org/I4210088191"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5035008543","https://openalex.org/A5100352324"],"corresponding_institution_ids":["https://openalex.org/I100135526","https://openalex.org/I4210088191","https://openalex.org/I4210149137"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.1895,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.77775197,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"22","issue":"1","first_page":"158","last_page":"158"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8956999778747559,"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":0.8956999778747559,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.016200000420212746,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.009600000455975533,"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":0.9180853366851807},{"id":"https://openalex.org/keywords/jaccard-index","display_name":"Jaccard index","score":0.6970593929290771},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6681492328643799},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5920355916023254},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5899092555046082},{"id":"https://openalex.org/keywords/scaffold","display_name":"Scaffold","score":0.5007674694061279},{"id":"https://openalex.org/keywords/contiguity","display_name":"Contiguity","score":0.49610528349876404},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.446937620639801},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4171859323978424},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27697959542274475},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.24477934837341309},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1634807586669922},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.15867024660110474},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1532720923423767},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14203467965126038},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08355426788330078}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.9180853366851807},{"id":"https://openalex.org/C203519979","wikidata":"https://www.wikidata.org/wiki/Q865360","display_name":"Jaccard index","level":3,"score":0.6970593929290771},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6681492328643799},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5920355916023254},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5899092555046082},{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.5007674694061279},{"id":"https://openalex.org/C68767595","wikidata":"https://www.wikidata.org/wiki/Q1677999","display_name":"Contiguity","level":2,"score":0.49610528349876404},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.446937620639801},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4171859323978424},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27697959542274475},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.24477934837341309},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1634807586669922},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.15867024660110474},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1532720923423767},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14203467965126038},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08355426788330078},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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/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},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"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":"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":"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-021-04081-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04081-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04081-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33765921","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33765921","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:da6b9498ac734be4953f754aa8348988","is_oa":true,"landing_page_url":"https://doaj.org/article/da6b9498ac734be4953f754aa8348988","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-16 (2021)","raw_type":"article"},{"id":"pmh:oai:eprints.qut.edu.au:230460","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402607","display_name":"QUT ePrints (Queensland University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I160993911","host_organization_name":"Queensland University of Technology","host_organization_lineage":["https://openalex.org/I160993911"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Contribution to Journal"},{"id":"pmh:oai:pubmedcentral.nih.gov:7993450","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7993450","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04081-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04081-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04081-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6553891117","display_name":null,"funder_award_id":"2018YFD0900301-05","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7987138276","display_name":null,"funder_award_id":"2018YFD0900301","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3139503429.pdf","grobid_xml":"https://content.openalex.org/works/W3139503429.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W2008826985","https://openalex.org/W2022986961","https://openalex.org/W2026345779","https://openalex.org/W2036815225","https://openalex.org/W2073569203","https://openalex.org/W2081770828","https://openalex.org/W2102021831","https://openalex.org/W2103441770","https://openalex.org/W2107772251","https://openalex.org/W2129744420","https://openalex.org/W2129933858","https://openalex.org/W2130530163","https://openalex.org/W2132069633","https://openalex.org/W2159794180","https://openalex.org/W2171531867","https://openalex.org/W2264578395","https://openalex.org/W2266485219","https://openalex.org/W2322902521","https://openalex.org/W2428569935","https://openalex.org/W2607669908","https://openalex.org/W2767132092","https://openalex.org/W2789843538","https://openalex.org/W2897233545","https://openalex.org/W2905454979","https://openalex.org/W2927036568","https://openalex.org/W2948487375","https://openalex.org/W2949059287","https://openalex.org/W2950354111","https://openalex.org/W2950469833","https://openalex.org/W2950682063","https://openalex.org/W2951265437","https://openalex.org/W2952789401","https://openalex.org/W2955099493","https://openalex.org/W2975030516","https://openalex.org/W3044926932","https://openalex.org/W3087414372","https://openalex.org/W6783532490"],"related_works":["https://openalex.org/W2089480001","https://openalex.org/W3167837387","https://openalex.org/W2885619582","https://openalex.org/W54719527","https://openalex.org/W4250462852","https://openalex.org/W2944010518","https://openalex.org/W2993223466","https://openalex.org/W2105191441","https://openalex.org/W2589404674","https://openalex.org/W3110957961"],"abstract_inverted_index":{"BACKGROUND:":[0],"Synthetic":[1],"long":[2,123],"reads":[3],"(SLR)":[4],"with":[5,31,91],"long-range":[6],"co-barcoding":[7,59],"information":[8],"are":[9],"now":[10],"widely":[11],"applied":[12,116],"in":[13,55,111],"genomics":[14],"research.":[15],"Although":[16],"several":[17],"tools":[18],"have":[19],"been":[20],"developed":[21,45],"for":[22,36,162],"each":[23],"specific":[24],"SLR":[25,153],"technique,":[26],"a":[27,46,69,100,119,188,193],"robust":[28],"standalone":[29,47],"scaffolder":[30],"high":[32],"efficiency":[33],"is":[34,175],"warranted":[35],"hybrid":[37,194],"genome":[38],"assembly.":[39,114],"RESULTS:":[40],"In":[41],"this":[42,148],"work,":[43],"we":[44],"scaffolding":[48],"tool,":[49],"SLR-superscaffolder,":[50],"to":[51,77,103,118],"link":[52],"together":[53],"contigs":[54,110,145,164],"draft":[56,136,189],"assemblies":[57],"using":[58],"and":[60,81,85,128,158],"paired-end":[61,95],"read":[62,125],"information.":[63,96],"Our":[64],"top-to-bottom":[65],"scheme":[66],"first":[67],"builds":[68],"global":[70],"scaffold":[71,131],"graph":[72],"based":[73],"on":[74,142],"Jaccard":[75],"Similarity":[76],"determine":[78],"the":[79,89,92,105,112,130,185],"order":[80],"orientation":[82],"of":[83,94,108,133,173,187],"contigs,":[84],"then":[86],"locally":[87],"improves":[88],"scaffolds":[90],"aid":[93],"We":[97,115],"also":[98],"exploited":[99],"screening":[101],"algorithm":[102],"reduce":[104],"negative":[106],"effect":[107],"misassembled":[109],"input":[113,144],"SLR-superscaffolder":[117,174,181],"human":[120],"single":[121],"tube":[122],"fragment":[124],"sequencing":[126,168],"dataset":[127],"increased":[129],"NG50":[132],"its":[134],"corresponding":[135],"assembly":[137,190,195],"1349":[138],"fold.":[139],"Moreover,":[140],"benchmarking":[141],"different":[143],"showed":[146],"that":[147],"approach":[149],"overall":[150],"outperformed":[151],"existing":[152],"scaffolders,":[154],"providing":[155],"longer":[156],"contiguity":[157,186],"fewer":[159],"misassemblies,":[160],"especially":[161],"short":[163],"assembled":[165],"by":[166,191],"next-generation":[167],"data.":[169],"The":[170],"open-source":[171],"code":[172],"available":[176],"at":[177],"https://github.com/BGI-Qingdao/SLR-superscaffolder":[178],".":[179],"CONCLUSIONS:":[180],"can":[182],"dramatically":[183],"improve":[184],"integrating":[192],"strategy.":[196]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
