{"id":"https://openalex.org/W4288044945","doi":null,"title":"Inverted Repeats Scaffolding for a Dedicated Chloroplast Genome Assembler","display_name":"Inverted Repeats Scaffolding for a Dedicated Chloroplast Genome Assembler","publication_year":2022,"publication_date":"2022-06-03","ids":{"openalex":"https://openalex.org/W4288044945"},"language":"en","primary_location":{"id":"pmh:oai:HAL:hal-03684406v1","doi":null,"is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03684406v1/document","pdf_url":"https://inria.hal.science/hal-03684406/document","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2022","raw_type":"info:eu-repo/semantics/preprint"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://inria.hal.science/hal-03684406/document","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":[{"id":"https://openalex.org/I3017942884","display_name":"Institut de Math\u00e9matiques de Jussieu-Paris Rive Gauche","ror":"https://ror.org/03fk87k11","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I3017942884","https://openalex.org/I39804081","https://openalex.org/I4210141950"]},{"id":"https://openalex.org/I4405258500","display_name":"GENSCALE: Algorithmes pour les donn\u00e9es g\u00e9nomiques : passage \u00e0 l'\u00e9chelle, pr\u00e9cision, frugalit\u00e9","ror":"https://ror.org/00rttk466","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210133778","https://openalex.org/I4210159245","https://openalex.org/I4405258500","https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Epain, Victor","raw_affiliation_strings":["GenScale - Scalable, Optimized and Parallel Algorithms for Genomics (Campus de Beaulieu 35042 Rennes cedex - France)","Institut de Math\u00e9matiques de Jussieu - Paris Rive Gauche"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GenScale - Scalable, Optimized and Parallel Algorithms for Genomics (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":["https://openalex.org/I4405258500"]},{"raw_affiliation_string":"Institut de Math\u00e9matiques de Jussieu - Paris Rive Gauche","institution_ids":["https://openalex.org/I3017942884"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160058439","display_name":"Dominique Lavenier","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258500","display_name":"GENSCALE: Algorithmes pour les donn\u00e9es g\u00e9nomiques : passage \u00e0 l'\u00e9chelle, pr\u00e9cision, frugalit\u00e9","ror":"https://ror.org/00rttk466","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210133778","https://openalex.org/I4210159245","https://openalex.org/I4405258500","https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Lavenier, Dominique","raw_affiliation_strings":["GenScale - Scalable, Optimized and Parallel Algorithms for Genomics (Campus de Beaulieu 35042 Rennes cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GenScale - Scalable, Optimized and Parallel Algorithms for Genomics (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":["https://openalex.org/I4405258500"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040381671","display_name":"Rumen Andonov","orcid":"https://orcid.org/0000-0003-4842-7102","observed_orcids":["https://orcid.org/0000-0003-4842-7102"]},"institutions":[{"id":"https://openalex.org/I4405258500","display_name":"GENSCALE: Algorithmes pour les donn\u00e9es g\u00e9nomiques : passage \u00e0 l'\u00e9chelle, pr\u00e9cision, frugalit\u00e9","ror":"https://ror.org/00rttk466","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210133778","https://openalex.org/I4210159245","https://openalex.org/I4405258500","https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Andonov, Rumen","raw_affiliation_strings":["GenScale - Scalable, Optimized and Parallel Algorithms for Genomics (Campus de Beaulieu 35042 Rennes cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GenScale - Scalable, Optimized and Parallel Algorithms for Genomics (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":["https://openalex.org/I4405258500"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5064046379"],"corresponding_institution_ids":["https://openalex.org/I3017942884","https://openalex.org/I4405258500"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":3,"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":0.9496999979019165,"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":0.9496999979019165,"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":0.017500000074505806,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.01640000008046627,"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/chloroplast-genome-assembly","display_name":"chloroplast genome assembly","score":0.9980000257492065},{"id":"https://openalex.org/keywords/scaffolding","display_name":"scaffolding","score":0.8859999775886536},{"id":"https://openalex.org/keywords/inverted-repeats","display_name":"inverted repeats","score":0.9810000061988831},{"id":"https://openalex.org/keywords/de-bruijn-graph","display_name":"de Bruijn graph","score":0.7960000038146973},{"id":"https://openalex.org/keywords/integer-linear-programming","display_name":"integer linear programming","score":0.9440000057220459},{"id":"https://openalex.org/keywords/np-completeness","display_name":"NP-completeness","score":0.9760000109672546},{"id":"https://openalex.org/keywords/branch-and-bound","display_name":"branch and bound","score":0.9100000262260437}],"concepts":[{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.73580402135849},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.6548821926116943},{"id":"https://openalex.org/C2779557605","wikidata":"https://www.wikidata.org/wiki/Q9890","display_name":"Omega","level":2,"score":0.629208505153656},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.5538290739059448},{"id":"https://openalex.org/C29248071","wikidata":"https://www.wikidata.org/wiki/Q163310","display_name":"Turing machine","level":3,"score":0.5505233407020569},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.5145627856254578},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.44928738474845886},{"id":"https://openalex.org/C197551870","wikidata":"https://www.wikidata.org/wiki/Q7617809","display_name":"Stochastic Petri net","level":3,"score":0.4460078477859497},{"id":"https://openalex.org/C112680207","wikidata":"https://www.wikidata.org/wiki/Q714886","display_name":"Regular polygon","level":2,"score":0.41708019375801086},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.18127551674842834},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.14827492833137512},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1231236457824707},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:HAL:hal-03684406v1","doi":null,"is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03684406v1/document","pdf_url":"https://inria.hal.science/hal-03684406/document","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2022","raw_type":"info:eu-repo/semantics/preprint"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-03684406v1","doi":null,"is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03684406v1/document","pdf_url":"https://inria.hal.science/hal-03684406/document","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2022","raw_type":"info:eu-repo/semantics/preprint"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4288044945.pdf","grobid_xml":"https://content.openalex.org/works/W4288044945.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1487687089","https://openalex.org/W2042219261","https://openalex.org/W2107772251","https://openalex.org/W2179933869","https://openalex.org/W2233296499","https://openalex.org/W2413160458","https://openalex.org/W2535995078","https://openalex.org/W2604269101","https://openalex.org/W2607327662","https://openalex.org/W2610986153","https://openalex.org/W2934640744","https://openalex.org/W2945963500","https://openalex.org/W3091292540","https://openalex.org/W3193005861"],"related_works":["https://openalex.org/W4300539066","https://openalex.org/W4390849332","https://openalex.org/W4285533641","https://openalex.org/W4391575695","https://openalex.org/W7054838164","https://openalex.org/W2945963500","https://openalex.org/W4200247799","https://openalex.org/W4393395633","https://openalex.org/W2780320090","https://openalex.org/W7220959395"],"abstract_inverted_index":{"This":[0],"paper":[1],"describes":[2],"a":[3,41,51,91,143],"novel":[4],"assembly":[5],"approach":[6,46],"for":[7],"chloroplast":[8,82,152],"genomes.":[9],"It":[10,103],"contains":[11],"two":[12],"modular":[13],"steps.":[14],"In":[15],"the":[16,21,30,34,67,70,73,79,95,127,164,167,172,205],"first":[17,206],"step,":[18],"based":[19,45],"on":[20,142,181],"hypothesis":[22],"that":[23,81,121,156],"chloroplasts":[24],"genomes":[25,83],"are":[26,59],"over-represented":[27],"compared":[28],"to":[29,105,163],"nuclear":[31],"genome":[32],"in":[33],"plant's":[35],"cell,":[36],"we":[37,89,119,129,178],"assemble":[38,106],"contigs":[39,58,74],"with":[40,50,161],"De":[42],"Bruijn":[43],"graph":[44],"using":[47],"short":[48],"reads":[49],"high":[52],"k-mer":[53],"coverage.":[54],"Connections":[55],"between":[56],"oriented":[57],"also":[60],"provided":[61],"here.":[62],"The":[63,186],"second":[64],"step":[65],"determines":[66],"order":[68],"and":[69,118,131,154],"orientation":[71],"of":[72,78,94,145,150,166,174,192],"(scaffolding).":[75],"Taking":[76],"advantage":[77],"knowledge":[80],"posses":[84],"well":[85],"studied":[86],"circular":[87],"structure,":[88],"develop":[90],"particular":[92],"formulation":[93,195],"scaffolding":[96,176],"problem,":[97],"called":[98],"Nested":[99],"Inverted":[100],"Fragments":[101],"Scaffolding.":[102],"aims":[104],"highly":[107],"conserved":[108],"inverted":[109],"repeats.":[110],"We":[111,138],"formulate":[112],"it":[113,122,157,180],"as":[114,196],"an":[115,133,189],"optimisation":[116],"problem":[117,128],"prove":[120],"is":[123],"NP-Complete.":[124],"To":[125,169],"solve":[126],"propose":[130],"implement":[132],"integer":[134,194],"linear":[135],"programming":[136],"formulation.":[137],"evaluate":[139],"our":[140,175,193],"method":[141],"set":[144],"real":[146],"instances":[147,200],"(a":[148],"benchmark":[149],"42":[151],"genomes)":[153],"show":[155],"obtains":[158],"notable":[159],"achievements":[160],"respect":[162],"quality":[165],"results.":[168],"further":[170],"estimate":[171],"performance":[173],"module,":[177],"test":[179],"huge":[182],"artificially":[183],"created":[184],"instances.":[185],"results":[187],"demonstrate":[188],"excellent":[190],"behaviour":[191],"even":[197],"very":[198],"large":[199],"have":[201],"been":[202],"solved":[203],"at":[204],"Branch":[207],"&":[208],"Bounds":[209],"node.":[210]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2022-07-27T00:00:00"}
