{"id":"https://openalex.org/W2962743744","doi":"https://doi.org/10.1093/bioinformatics/btx370","title":"A spectral algorithm for fast <i>de novo</i> layout of uncorrected long nanopore reads","display_name":"A spectral algorithm for fast <i>de novo</i> layout of uncorrected long nanopore reads","publication_year":2017,"publication_date":"2017-06-06","ids":{"openalex":"https://openalex.org/W2962743744","doi":"https://doi.org/10.1093/bioinformatics/btx370","mag":"2962743744"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx370","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/20/3188/25165728/btx370.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":["arxiv","crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/20/3188/25165728/btx370.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090065520","display_name":"Antoine Recanati","orcid":null},"institutions":[{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"funder","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Antoine Recanati","raw_affiliation_strings":["CNRS & D.I., UMR 8548, \u00c9cole Normale Sup\u00e9rieure, Paris, France"],"affiliations":[{"raw_affiliation_string":"CNRS & D.I., UMR 8548, \u00c9cole Normale Sup\u00e9rieure, Paris, France","institution_ids":["https://openalex.org/I29607241","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067751149","display_name":"Thomas Br\u00fcls","orcid":"https://orcid.org/0000-0003-3525-8979"},"institutions":[{"id":"https://openalex.org/I2738703131","display_name":"Commissariat \u00e0 l'\u00c9nergie Atomique et aux \u00c9nergies Alternatives","ror":"https://ror.org/00jjx8s55","country_code":"FR","type":"funder","lineage":["https://openalex.org/I2738703131"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210115028","display_name":"Genoscope","ror":"https://ror.org/028pnqf58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210115028"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210113668","display_name":"Direction de la Recherche Fondamentale","ror":"https://ror.org/01yvj5k91","country_code":"FR","type":"facility","lineage":["https://openalex.org/I2738703131","https://openalex.org/I4210113668"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Thomas Br\u00fcls","raw_affiliation_strings":["Commissariat \u00e0 l\u2019Energie Atomique et aux Energies Alternatives, Direction de la Recherche Fondamentale, Genoscope","UMR 8030, Centre National de la Recherche Scientifique, Universit\u00e9 Paris-Saclay, Evry, France","Universit\u00e9 Paris-Saclay, Evry, France"],"affiliations":[{"raw_affiliation_string":"Commissariat \u00e0 l\u2019Energie Atomique et aux Energies Alternatives, Direction de la Recherche Fondamentale, Genoscope","institution_ids":["https://openalex.org/I2738703131","https://openalex.org/I4210113668","https://openalex.org/I4210115028"]},{"raw_affiliation_string":"UMR 8030, Centre National de la Recherche Scientifique, Universit\u00e9 Paris-Saclay, Evry, France","institution_ids":["https://openalex.org/I277688954","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Evry, France","institution_ids":["https://openalex.org/I277688954"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063516752","display_name":"Alexandre d\u2019Aspremont","orcid":"https://orcid.org/0000-0003-3851-216X"},"institutions":[{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"funder","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Alexandre d\u2019Aspremont","raw_affiliation_strings":["CNRS & D.I., UMR 8548, \u00c9cole Normale Sup\u00e9rieure, Paris, France","Statistical Machine Learning and Parsimony"],"affiliations":[{"raw_affiliation_string":"CNRS & D.I., UMR 8548, \u00c9cole Normale Sup\u00e9rieure, Paris, France","institution_ids":["https://openalex.org/I29607241","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Statistical Machine Learning and Parsimony","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5090065520"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I29607241"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4253,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.62894319,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"33","issue":"20","first_page":"3188","last_page":"3194"},"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":0.9836999773979187,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9779000282287598,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.9204916954040527},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.8986598253250122},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.8587446212768555},{"id":"https://openalex.org/keywords/nanopore","display_name":"Nanopore","score":0.7245256900787354},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7156245112419128},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4916990399360657},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.4522542953491211},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4359840750694275},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4259011149406433},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17029133439064026},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12216612696647644},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10291564464569092},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.09556964039802551}],"concepts":[{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.9204916954040527},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.8986598253250122},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.8587446212768555},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.7245256900787354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7156245112419128},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4916990399360657},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.4522542953491211},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4359840750694275},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4259011149406433},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17029133439064026},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12216612696647644},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10291564464569092},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.09556964039802551},{"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},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx370","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/20/3188/25165728/btx370.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":"pmh:oai:arXiv.org:1609.07293","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1609.07293","pdf_url":"https://arxiv.org/pdf/1609.07293","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx370","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/20/3188/25165728/btx370.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":[{"score":0.6899999976158142,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320312414","display_name":"Oxford Nanopore Technologies","ror":"https://ror.org/04hyfx005"},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2962743744.pdf","grobid_xml":"https://content.openalex.org/works/W2962743744.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W344138311","https://openalex.org/W1519765314","https://openalex.org/W1527507758","https://openalex.org/W1579534339","https://openalex.org/W1635391495","https://openalex.org/W1982579644","https://openalex.org/W1983403167","https://openalex.org/W2006935644","https://openalex.org/W2056056197","https://openalex.org/W2102330006","https://openalex.org/W2107282968","https://openalex.org/W2107320771","https://openalex.org/W2107772251","https://openalex.org/W2120575449","https://openalex.org/W2121364424","https://openalex.org/W2123625124","https://openalex.org/W2131852975","https://openalex.org/W2142113273","https://openalex.org/W2157888653","https://openalex.org/W2189047836","https://openalex.org/W2194172909","https://openalex.org/W2337261418","https://openalex.org/W2575750030","https://openalex.org/W2598785105","https://openalex.org/W2952756608","https://openalex.org/W2952803933","https://openalex.org/W6634542447","https://openalex.org/W6687221489","https://openalex.org/W6732409900"],"related_works":["https://openalex.org/W3009176350","https://openalex.org/W1519765314","https://openalex.org/W2127651281","https://openalex.org/W2949198880","https://openalex.org/W2952788979","https://openalex.org/W2763726643","https://openalex.org/W3090794301","https://openalex.org/W4210830088","https://openalex.org/W3005683565","https://openalex.org/W2607669908"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"New":[2],"long":[3],"read":[4],"sequencers":[5],"promise":[6],"to":[7,33,50,71,85],"transform":[8],"sequencing":[9],"and":[10,28,46,56,102],"genome":[11],"assembly":[12,27,39,65],"by":[13],"producing":[14],"reads":[15,36,75],"tens":[16],"of":[17],"kilobases":[18],"long.":[19],"However,":[20],"their":[21],"high":[22],"error":[23],"rate":[24],"significantly":[25],"complicates":[26],"requires":[29],"expensive":[30],"correction":[31],"steps":[32],"layout":[34,51],"the":[35,52,86,96],"using":[37],"standard":[38],"engines.":[40],"Results":[41],"We":[42],"present":[43],"an":[44],"original":[45],"efficient":[47],"spectral":[48],"algorithm":[49],"uncorrected":[53],"nanopore":[54],"reads,":[55],"its":[57],"seamless":[58],"integration":[59],"into":[60,80],"a":[61],"straightforward":[62],"overlap/layout/consensus":[63],"(OLC)":[64],"scheme.":[66],"The":[67],"method":[68],"is":[69],"shown":[70],"assemble":[72],"Oxford":[73],"Nanopore":[74],"from":[76,95],"several":[77],"bacterial":[78],"genomes":[79],"good":[81],"quality":[82],"(\u223c99%":[83],"identity":[84],"reference)":[87],"genome-sized":[88],"contigs,":[89],"while":[90],"yielding":[91],"more":[92],"fragmented":[93],"assemblies":[94],"eukaryotic":[97],"microbe":[98],"Sacharomyces":[99],"cerevisiae.":[100],"Availability":[101],"implementation":[103],"https://github.com/antrec/spectrassembler.":[104],"Supplementary":[105,107],"Information":[106],"data":[108],"are":[109],"available":[110],"at":[111],"Bioinformatics":[112],"online.":[113]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2019-07-30T00:00:00"}