{"id":"https://openalex.org/W2129744420","doi":"https://doi.org/10.1093/bioinformatics/btq683","title":"Scaffolding pre-assembled contigs using SSPACE","display_name":"Scaffolding pre-assembled contigs using SSPACE","publication_year":2010,"publication_date":"2010-12-12","ids":{"openalex":"https://openalex.org/W2129744420","doi":"https://doi.org/10.1093/bioinformatics/btq683","mag":"2129744420","pmid":"https://pubmed.ncbi.nlm.nih.gov/21149342"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq683","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq683","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/4/578/48866383/bioinformatics_27_4_578.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/4/578/48866383/bioinformatics_27_4_578.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063484441","display_name":"Marten Boetzer","orcid":null},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Marten Boetzer","raw_affiliation_strings":["1 BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, 2Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 11, 2333 CA Leiden and 3ZF-screens B.V., Niels Bohrweg 11, 2333 CA Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"1 BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, 2Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 11, 2333 CA Leiden and 3ZF-screens B.V., Niels Bohrweg 11, 2333 CA Leiden, The Netherlands","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047504832","display_name":"Christiaan V. Henkel","orcid":"https://orcid.org/0000-0001-9838-8215"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Christiaan V. Henkel","raw_affiliation_strings":["1 BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, 2Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 11, 2333 CA Leiden and 3ZF-screens B.V., Niels Bohrweg 11, 2333 CA Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"1 BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, 2Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 11, 2333 CA Leiden and 3ZF-screens B.V., Niels Bohrweg 11, 2333 CA Leiden, The Netherlands","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063286596","display_name":"Hans J. Jansen","orcid":"https://orcid.org/0000-0002-8563-4146"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Hans J. Jansen","raw_affiliation_strings":["1 BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, 2Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 11, 2333 CA Leiden and 3ZF-screens B.V., Niels Bohrweg 11, 2333 CA Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"1 BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, 2Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 11, 2333 CA Leiden and 3ZF-screens B.V., Niels Bohrweg 11, 2333 CA Leiden, The Netherlands","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078897312","display_name":"Derek Butler","orcid":null},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Derek Butler","raw_affiliation_strings":["1 BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, 2Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 11, 2333 CA Leiden and 3ZF-screens B.V., Niels Bohrweg 11, 2333 CA Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"1 BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, 2Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 11, 2333 CA Leiden and 3ZF-screens B.V., Niels Bohrweg 11, 2333 CA Leiden, The Netherlands","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016959285","display_name":"Walter Pirovano","orcid":"https://orcid.org/0000-0002-2717-4735"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Walter Pirovano","raw_affiliation_strings":["1 BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, 2Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 11, 2333 CA Leiden and 3ZF-screens B.V., Niels Bohrweg 11, 2333 CA Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"1 BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, 2Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 11, 2333 CA Leiden and 3ZF-screens B.V., Niels Bohrweg 11, 2333 CA Leiden, The Netherlands","institution_ids":["https://openalex.org/I121797337"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5063484441"],"corresponding_institution_ids":["https://openalex.org/I121797337"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":20.4103,"has_fulltext":true,"cited_by_count":2493,"citation_normalized_percentile":{"value":0.99681781,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"27","issue":"4","first_page":"578","last_page":"579"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991999864578247,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9908999800682068,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.9537580013275146},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.7237880229949951},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6029034852981567},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5896843075752258},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5480631589889526},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.5420199036598206},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.48388370871543884},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41912710666656494},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40762192010879517},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29487287998199463},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.09558603167533875},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08718472719192505}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.9537580013275146},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.7237880229949951},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6029034852981567},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5896843075752258},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5480631589889526},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.5420199036598206},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.48388370871543884},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41912710666656494},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40762192010879517},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29487287998199463},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.09558603167533875},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08718472719192505},{"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/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":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":"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":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btq683","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq683","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/4/578/48866383/bioinformatics_27_4_578.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21149342","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21149342","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq683","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq683","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/4/578/48866383/bioinformatics_27_4_578.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2129744420.pdf","grobid_xml":"https://content.openalex.org/works/W2129744420.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1966822396","https://openalex.org/W2124985265","https://openalex.org/W2143063533","https://openalex.org/W2159946869","https://openalex.org/W2171475724","https://openalex.org/W2171531867"],"related_works":["https://openalex.org/W2127651281","https://openalex.org/W3167837387","https://openalex.org/W2993223466","https://openalex.org/W2949198880","https://openalex.org/W2944010518","https://openalex.org/W2157888653","https://openalex.org/W2131813051","https://openalex.org/W2613464961","https://openalex.org/W2089480001","https://openalex.org/W2313863482"],"abstract_inverted_index":{"De":[0],"novo":[1,64],"assembly":[2,65],"tools":[3,66],"play":[4],"a":[5,19,50,75,82,94],"main":[6],"role":[7],"in":[8,53,62],"reconstructing":[9],"genomes":[10],"from":[11],"next-generation":[12],"sequencing":[13,25],"(NGS)":[14],"data":[15,26],"and":[16,35,39,67,106,121],"usually":[17],"yield":[18],"number":[20],"of":[21,37,85,100,128],"contigs.":[22],"Using":[23],"paired-read":[24,89],"it":[27],"is":[28,49,81],"possible":[29,107],"to":[30],"assess":[31],"the":[32,46,126],"order,":[33],"distance":[34],"orientation":[36],"contigs":[38,87,130],"combine":[40],"them":[41],"into":[42],"so-called":[43],"scaffolds.":[44],"Although":[45],"latter":[47],"process":[48],"crucial":[51],"step":[52],"finishing":[54],"genomes,":[55],"scaffolding":[56],"algorithms":[57],"are":[58],"often":[59],"built-in":[60],"functions":[61],"de":[63],"cannot":[68],"be":[69],"independently":[70],"controlled.":[71],"We":[72],"here":[73],"present":[74],"new":[76],"tool,":[77],"called":[78],"SSPACE,":[79],"which":[80],"stand-alone":[83],"scaffolder":[84],"pre-assembled":[86],"using":[88],"data.":[90],"Main":[91],"features":[92],"are:":[93],"short":[95],"runtime,":[96],"multiple":[97],"library":[98],"input":[99],"paired-end":[101],"and/or":[102],"mate":[103],"pair":[104],"datasets":[105],"contig":[108],"extension":[109],"with":[110],"unmapped":[111],"sequence":[112],"reads.":[113],"SSPACE":[114],"shows":[115],"promising":[116],"results":[117],"on":[118],"both":[119],"prokaryote":[120],"eukaryote":[122],"genomic":[123],"testsets":[124],"where":[125],"amount":[127],"initial":[129],"was":[131],"reduced":[132],"by":[133],"at":[134],"least":[135],"75%.":[136]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":64},{"year":2024,"cited_by_count":120},{"year":2023,"cited_by_count":111},{"year":2022,"cited_by_count":187},{"year":2021,"cited_by_count":261},{"year":2020,"cited_by_count":239},{"year":2019,"cited_by_count":248},{"year":2018,"cited_by_count":269},{"year":2017,"cited_by_count":262},{"year":2016,"cited_by_count":218},{"year":2015,"cited_by_count":201},{"year":2014,"cited_by_count":145},{"year":2013,"cited_by_count":86},{"year":2012,"cited_by_count":55}],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2025-10-10T00:00:00"}
