{"id":"https://openalex.org/W4287756331","doi":null,"title":"DNA fragments positioning improvement to realise consensus sequences in the de novo long reads assembly context","display_name":"DNA fragments positioning improvement to realise consensus sequences in the de novo long reads assembly context","publication_year":2020,"publication_date":"2020-06-16","ids":{"openalex":"https://openalex.org/W4287756331"},"language":"en","primary_location":{"id":"pmh:oai:HAL:hal-03119772v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.inria.fr/hal-03119772","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://hal.inria.fr/hal-03119772","raw_type":"info:eu-repo/semantics/masterThesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal.inria.fr/hal-03119772","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064046379","display_name":"Victor Epain","orcid":"https://orcid.org/0000-0003-0049-0954","observed_orcids":["https://orcid.org/0000-0003-0049-0954"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Epain, Victor","raw_affiliation_strings":["Scalable, Optimized and Parallel Algorithms for Genomics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Scalable, Optimized and Parallel Algorithms for Genomics","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5064046379"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9951000213623047,"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":0.9951000213623047,"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":0.0027000000700354576,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.0008999999845400453,"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/de-novo-genome-assembly","display_name":"de novo genome assembly","score":0.8059999942779541},{"id":"https://openalex.org/keywords/long-reads","display_name":"long reads","score":0.7360000014305115},{"id":"https://openalex.org/keywords/consensus-sequence","display_name":"consensus sequence","score":0.7229999899864197},{"id":"https://openalex.org/keywords/indels","display_name":"indels","score":0.7009999752044678},{"id":"https://openalex.org/keywords/sequencing-errors","display_name":"sequencing errors","score":0.8820000290870667},{"id":"https://openalex.org/keywords/mixed-integer-linear-programming","display_name":"mixed-integer linear programming","score":0.9879999756813049},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"multiple sequence alignment","score":0.8690000176429749},{"id":"https://openalex.org/keywords/bacterial-genomes","display_name":"bacterial genomes","score":0.8149999976158142}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5705082416534424},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5049927830696106},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4535272717475891},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.45136311650276184},{"id":"https://openalex.org/C54985914","wikidata":"https://www.wikidata.org/wiki/Q1295754","display_name":"Consensus sequence","level":4,"score":0.4496132731437683},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.42918241024017334},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3927188813686371},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.367607444524765},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3370686173439026},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.18062731623649597},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14526093006134033},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.08233872056007385},{"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":[],"locations_count":1,"locations":[{"id":"pmh:oai:HAL:hal-03119772v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.inria.fr/hal-03119772","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://hal.inria.fr/hal-03119772","raw_type":"info:eu-repo/semantics/masterThesis"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-03119772v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.inria.fr/hal-03119772","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://hal.inria.fr/hal-03119772","raw_type":"info:eu-repo/semantics/masterThesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3099782484","https://openalex.org/W4310907668","https://openalex.org/W7097369121","https://openalex.org/W7047426708","https://openalex.org/W2344973950","https://openalex.org/W6931245289","https://openalex.org/W3022830479","https://openalex.org/W4238765644","https://openalex.org/W7100160329","https://openalex.org/W430114432"],"abstract_inverted_index":{"\\n":[0],"DNA":[1],"molecular":[2],"in":[3,9],"silico":[4],"analysis":[5],"requires":[6],"sequencing":[7,20,42],"it":[8,168],"fragments":[10],"called":[11],"reads,":[12],"and":[13,105,133,146,180],"then":[14,106,181],"assembling":[15],"them.":[16],"Today\u2019s,":[17],"long":[18],"reads":[19,80,97],"technologies":[21],"offer":[22],"the":[23,79,94,113,123,127,139,151,154,162,170,183,189,195,203,211,214],"possibility":[24],"to":[25,66,93,112,175],"overcome":[26],"genome\u2019s":[27],"repeated":[28],"regions":[29],"issues":[30],"with":[31,41,126,143,191],"being":[32],"entirely":[33],"covered,":[34],"but":[35,209],"product":[36],"high":[37],"errors":[38],"rate":[39],"data":[40],"errors,":[43],"like":[44],"nucleotides":[45],"insertions":[46],"or":[47,75],"deletions,called":[48],"indels.":[49],"De":[50,72],"novo":[51],"assembly":[52,55,164],"is":[53],"an":[54],"without":[56],"using":[57,71],"a":[58,85,98,101,108,120],"reference.":[59],"Although":[60],"some":[61],"assemblers":[62],"already":[63],"exist":[64],"according":[65,169],"several":[67],"methods":[68],"-":[69],"as":[70],"Bruijn":[73],"graphs":[74],"by":[76],"correcting":[77],"iteratively":[78],"for":[81,122,138],"example,":[82],"we":[83,91,118,134,166,187],"propose":[84,119],"two":[86],"steps":[87],"strategy":[88,159,190],":":[89],"first,":[90],"attribute":[92],"maximum":[95],"of":[96,157,213],"position":[99],"on":[100],"same":[102],"positions":[103],"axis":[104],"weproduct":[107],"consensus":[109,140,204],"sequence":[110],"thanks":[111],"positioning.":[114,152],"At":[115],"these":[116],"aims,":[117],"modelling":[121],"positioning":[124,198],"issue":[125],"mixed":[128],"integer":[129],"linear":[130],"programming":[131],"(MILP),":[132],"present":[135],"first":[136],"ideas":[137],"sequences":[141,148],"production":[142],"MILP":[144],"too":[145],"multiple":[147],"alignment":[149],"from":[150],"As":[153],"final":[155],"aim":[156],"this":[158],"isto":[160],"formalize":[161],"genome":[163],"issue,":[165],"structured":[167],"mathematical":[171],"method,":[172],"that":[173,197],"permits":[174],"target":[176],"methodological":[177],"choices":[178],"precisely,":[179],"reducing":[182],"heuristic":[184],"uses.":[185],"Finally,":[186],"tested":[188],"bacteria":[192],"genomes.":[193],"Despite":[194],"fact":[196],"results":[199,205],"show":[200],"positive":[201,208],"ones,":[202],"are":[206],"less":[207],"don\u2019tremove":[210],"potentiality":[212],"associated":[215],"methods.\\n":[216]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2022-07-26T00:00:00"}