{"id":"https://openalex.org/W4392201117","doi":"https://doi.org/10.1038/s43588-024-00596-6","title":"Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA","display_name":"Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA","publication_year":2024,"publication_date":"2024-02-26","ids":{"openalex":"https://openalex.org/W4392201117","doi":"https://doi.org/10.1038/s43588-024-00596-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/38413777"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-024-00596-6","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-024-00596-6","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal.science/hal-04489740v1/file/2023.05.31.543043v4.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078221150","display_name":"T\u00e9o Lemane","orcid":"https://orcid.org/0000-0002-7210-3178"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"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":"government","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/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","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/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4210096708","display_name":"G\u00e9nomique M\u00e9tabolique du Genoscope","ror":"https://ror.org/00xc55v17","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I2738703131","https://openalex.org/I2738703131","https://openalex.org/I277688954","https://openalex.org/I4210096427","https://openalex.org/I4210096708","https://openalex.org/I4210113668","https://openalex.org/I88467170"]},{"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/I4210128565","display_name":"CEA Paris-Saclay","ror":"https://ror.org/03n15ch10","country_code":"FR","type":"government","lineage":["https://openalex.org/I2738703131","https://openalex.org/I277688954","https://openalex.org/I4210128565"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"T\u00e9o Lemane","raw_affiliation_strings":["G\u00e9nomique M\u00e9tabolique, Genoscope, Institut de Biologie Fran\u00e7ois Jacob, CEA, CNRS, Univ. Evry, Universit\u00e9 Paris-Saclay, Evry, France. teo.lemane@genoscope.cns.fr","Univ. Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, France. teo.lemane@genoscope.cns.fr","IRISA - Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires (Avenue du g\u00e9n\u00e9ral Leclerc\r\nCampus de Beaulieu \r\n35042 RENNES CEDEX - France)","UMR 8030 - G\u00e9nomique m\u00e9tabolique (GENOSCOPE, 2 rue Gaston Cr\u00e9mieux 91057 Evry Cedex - France)"],"affiliations":[{"raw_affiliation_string":"G\u00e9nomique M\u00e9tabolique, Genoscope, Institut de Biologie Fran\u00e7ois Jacob, CEA, CNRS, Univ. Evry, Universit\u00e9 Paris-Saclay, Evry, France. teo.lemane@genoscope.cns.fr","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210115028","https://openalex.org/I4210128565","https://openalex.org/I277688954","https://openalex.org/I2738703131"]},{"raw_affiliation_string":"Univ. Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, France. teo.lemane@genoscope.cns.fr","institution_ids":["https://openalex.org/I2802519937","https://openalex.org/I56067802","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"IRISA - Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires (Avenue du g\u00e9n\u00e9ral Leclerc\r\nCampus de Beaulieu \r\n35042 RENNES CEDEX - France)","institution_ids":["https://openalex.org/I2802519937"]},{"raw_affiliation_string":"UMR 8030 - G\u00e9nomique m\u00e9tabolique (GENOSCOPE, 2 rue Gaston Cr\u00e9mieux 91057 Evry Cedex - France)","institution_ids":["https://openalex.org/I4210096708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092087986","display_name":"Nolan Lezzoche","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I143002897","display_name":"Universit\u00e9 de Toulon","ror":"https://ror.org/02m9kbe37","country_code":"FR","type":"education","lineage":["https://openalex.org/I143002897"]},{"id":"https://openalex.org/I21491767","display_name":"Aix-Marseille Universit\u00e9","ror":"https://ror.org/035xkbk20","country_code":"FR","type":"education","lineage":["https://openalex.org/I21491767"]},{"id":"https://openalex.org/I4210155331","display_name":"Institut M\u00e9diterran\u00e9en d\u2019Oc\u00e9anologie","ror":"https://ror.org/05258q350","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I1327553481","https://openalex.org/I143002897","https://openalex.org/I154202486","https://openalex.org/I154202486","https://openalex.org/I21491767","https://openalex.org/I21491767","https://openalex.org/I2799535048","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210088668","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210090127","https://openalex.org/I4210093025","https://openalex.org/I4210113730","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210131494","https://openalex.org/I4210148025","https://openalex.org/I4210155331","https://openalex.org/I4210166444","https://openalex.org/I4210166444","https://openalex.org/I4405257220","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Nolan Lezzoche","raw_affiliation_strings":["Aix-Marseille Universit\u00e9, Universit\u00e9 de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France","MIO - Institut m\u00e9diterran\u00e9en d'oc\u00e9anologie (M.I.O. Institut M\u00e9diterran\u00e9en d'Oc\u00e9anologie \r\nB\u00e2timent M\u00e9diterran\u00e9e\r\n163 Avenue de Luminy\r\n13288 Marseille - France)"],"affiliations":[{"raw_affiliation_string":"Aix-Marseille Universit\u00e9, Universit\u00e9 de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France","institution_ids":["https://openalex.org/I4210155331","https://openalex.org/I143002897","https://openalex.org/I21491767","https://openalex.org/I4210166444","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"MIO - Institut m\u00e9diterran\u00e9en d'oc\u00e9anologie (M.I.O. Institut M\u00e9diterran\u00e9en d'Oc\u00e9anologie \r\nB\u00e2timent M\u00e9diterran\u00e9e\r\n163 Avenue de Luminy\r\n13288 Marseille - France)","institution_ids":["https://openalex.org/I4210155331"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016861943","display_name":"Julien Lecubin","orcid":"https://orcid.org/0000-0002-0090-4232"},"institutions":[{"id":"https://openalex.org/I2802931824","display_name":"Institut Pprime","ror":"https://ror.org/05vjdsn22","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I171246369","https://openalex.org/I2802931824","https://openalex.org/I32881790","https://openalex.org/I4210095849"]},{"id":"https://openalex.org/I4210116669","display_name":"Ch\u00e2teau Gombert","ror":"https://ror.org/02kspbq18","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210116669"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Julien Lecubin","raw_affiliation_strings":["SIP, OSU PYTHEAS, Marseille, France","OSU PYTHEAS - Institut Pyth\u00e9as (Technop\u00f4le de Ch\u00e2teau-Gombert\r\n38, rue Fr\u00e9d\u00e9ric Joliot-Curie\r\n13388 MARSEILLE cedex 13 - France)"],"affiliations":[{"raw_affiliation_string":"SIP, OSU PYTHEAS, Marseille, France","institution_ids":[]},{"raw_affiliation_string":"OSU PYTHEAS - Institut Pyth\u00e9as (Technop\u00f4le de Ch\u00e2teau-Gombert\r\n38, rue Fr\u00e9d\u00e9ric Joliot-Curie\r\n13388 MARSEILLE cedex 13 - France)","institution_ids":["https://openalex.org/I4210116669","https://openalex.org/I2802931824"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083406112","display_name":"\u00c9ric Pelletier","orcid":"https://orcid.org/0000-0003-4228-1712"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"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":"government","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/I4210096708","display_name":"G\u00e9nomique M\u00e9tabolique du Genoscope","ror":"https://ror.org/00xc55v17","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I2738703131","https://openalex.org/I2738703131","https://openalex.org/I277688954","https://openalex.org/I4210096427","https://openalex.org/I4210096708","https://openalex.org/I4210113668","https://openalex.org/I88467170"]},{"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/I4210128565","display_name":"CEA Paris-Saclay","ror":"https://ror.org/03n15ch10","country_code":"FR","type":"government","lineage":["https://openalex.org/I2738703131","https://openalex.org/I277688954","https://openalex.org/I4210128565"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Eric Pelletier","raw_affiliation_strings":["G\u00e9nomique M\u00e9tabolique, Genoscope, Institut de Biologie Fran\u00e7ois Jacob, CEA, CNRS, Univ. Evry, Universit\u00e9 Paris-Saclay, Evry, France","Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, CNRS, Paris, France","UMR 8030 - G\u00e9nomique m\u00e9tabolique (GENOSCOPE, 2 rue Gaston Cr\u00e9mieux 91057 Evry Cedex - France)","GOSEE - Global Oceans Systems Ecology & Evolution - Tara Oceans (3 rue Michel-Ange, 75016 Paris - France)"],"affiliations":[{"raw_affiliation_string":"G\u00e9nomique M\u00e9tabolique, Genoscope, Institut de Biologie Fran\u00e7ois Jacob, CEA, CNRS, Univ. Evry, Universit\u00e9 Paris-Saclay, Evry, France","institution_ids":["https://openalex.org/I4210115028","https://openalex.org/I277688954","https://openalex.org/I1294671590","https://openalex.org/I4210128565","https://openalex.org/I2738703131"]},{"raw_affiliation_string":"Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, CNRS, Paris, France","institution_ids":["https://openalex.org/I1294671590"]},{"raw_affiliation_string":"UMR 8030 - G\u00e9nomique m\u00e9tabolique (GENOSCOPE, 2 rue Gaston Cr\u00e9mieux 91057 Evry Cedex - France)","institution_ids":["https://openalex.org/I4210096708"]},{"raw_affiliation_string":"GOSEE - Global Oceans Systems Ecology & Evolution - Tara Oceans (3 rue Michel-Ange, 75016 Paris - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054300468","display_name":"Magali Lescot","orcid":"https://orcid.org/0000-0001-8189-0823"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I143002897","display_name":"Universit\u00e9 de Toulon","ror":"https://ror.org/02m9kbe37","country_code":"FR","type":"education","lineage":["https://openalex.org/I143002897"]},{"id":"https://openalex.org/I21491767","display_name":"Aix-Marseille Universit\u00e9","ror":"https://ror.org/035xkbk20","country_code":"FR","type":"education","lineage":["https://openalex.org/I21491767"]},{"id":"https://openalex.org/I4210155331","display_name":"Institut M\u00e9diterran\u00e9en d\u2019Oc\u00e9anologie","ror":"https://ror.org/05258q350","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I1327553481","https://openalex.org/I143002897","https://openalex.org/I154202486","https://openalex.org/I154202486","https://openalex.org/I21491767","https://openalex.org/I21491767","https://openalex.org/I2799535048","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210088668","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210090127","https://openalex.org/I4210093025","https://openalex.org/I4210113730","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210131494","https://openalex.org/I4210148025","https://openalex.org/I4210155331","https://openalex.org/I4210166444","https://openalex.org/I4210166444","https://openalex.org/I4405257220","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Magali Lescot","raw_affiliation_strings":["Aix-Marseille Universit\u00e9, Universit\u00e9 de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France","Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, CNRS, Paris, France","GOSEE - Global Oceans Systems Ecology & Evolution - Tara Oceans (3 rue Michel-Ange, 75016 Paris - France)","MIO - Institut m\u00e9diterran\u00e9en d'oc\u00e9anologie (M.I.O. Institut M\u00e9diterran\u00e9en d'Oc\u00e9anologie \r\nB\u00e2timent M\u00e9diterran\u00e9e\r\n163 Avenue de Luminy\r\n13288 Marseille - France)"],"affiliations":[{"raw_affiliation_string":"Aix-Marseille Universit\u00e9, Universit\u00e9 de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France","institution_ids":["https://openalex.org/I4210155331","https://openalex.org/I143002897","https://openalex.org/I21491767","https://openalex.org/I4210166444","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, CNRS, Paris, France","institution_ids":["https://openalex.org/I1294671590"]},{"raw_affiliation_string":"GOSEE - Global Oceans Systems Ecology & Evolution - Tara Oceans (3 rue Michel-Ange, 75016 Paris - France)","institution_ids":[]},{"raw_affiliation_string":"MIO - Institut m\u00e9diterran\u00e9en d'oc\u00e9anologie (M.I.O. Institut M\u00e9diterran\u00e9en d'Oc\u00e9anologie \r\nB\u00e2timent M\u00e9diterran\u00e9e\r\n163 Avenue de Luminy\r\n13288 Marseille - France)","institution_ids":["https://openalex.org/I4210155331"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058310668","display_name":"Rayan Chikhi","orcid":"https://orcid.org/0000-0003-1099-8735"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Rayan Chikhi","raw_affiliation_strings":["Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, G5 Sequence Bioinformatics, Paris, France","Algorithmes pour les s\u00e9quences biologiques - Sequence Bioinformatics (D\u00e9partement de Biologie Computationnelle - France)"],"affiliations":[{"raw_affiliation_string":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, G5 Sequence Bioinformatics, Paris, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I204730241"]},{"raw_affiliation_string":"Algorithmes pour les s\u00e9quences biologiques - Sequence Bioinformatics (D\u00e9partement de Biologie Computationnelle - France)","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012897398","display_name":"Pierre Peterlongo","orcid":"https://orcid.org/0000-0003-0776-6407"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","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/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4210133778","display_name":"Centre Inria de l'Universit\u00e9 de Rennes","ror":"https://ror.org/04040yw90","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210133778"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre Peterlongo","raw_affiliation_strings":["Univ. Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, France. pierre.peterlongo@inria.fr","IRISA - Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires (Avenue du g\u00e9n\u00e9ral Leclerc\r\nCampus de Beaulieu \r\n35042 RENNES CEDEX - France)"],"affiliations":[{"raw_affiliation_string":"Univ. Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, France. pierre.peterlongo@inria.fr","institution_ids":["https://openalex.org/I56067802","https://openalex.org/I1326498283","https://openalex.org/I4210133778","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"IRISA - Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires (Avenue du g\u00e9n\u00e9ral Leclerc\r\nCampus de Beaulieu \r\n35042 RENNES CEDEX - France)","institution_ids":["https://openalex.org/I2802519937"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5078221150"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2738703131","https://openalex.org/I277688954","https://openalex.org/I2802519937","https://openalex.org/I4210096708","https://openalex.org/I4210115028","https://openalex.org/I4210128565","https://openalex.org/I56067802"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":2.929,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.91119857,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"4","issue":"2","first_page":"104","last_page":"109"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9975000023841858,"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":0.9975000023841858,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9868999719619751,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9828000068664551,"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/search-engine-indexing","display_name":"Search engine indexing","score":0.787559986114502},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7593543529510498},{"id":"https://openalex.org/keywords/terabyte","display_name":"Terabyte","score":0.7166728973388672},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7017292380332947},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.5808162689208984},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.543262243270874},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5181726217269897},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48040130734443665},{"id":"https://openalex.org/keywords/fraction","display_name":"Fraction (chemistry)","score":0.4750088155269623},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.4228825867176056},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3047821819782257},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.254552960395813},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11553364992141724}],"concepts":[{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.787559986114502},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7593543529510498},{"id":"https://openalex.org/C199683683","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Terabyte","level":2,"score":0.7166728973388672},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7017292380332947},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.5808162689208984},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.543262243270874},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5181726217269897},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48040130734443665},{"id":"https://openalex.org/C149629883","wikidata":"https://www.wikidata.org/wiki/Q660926","display_name":"Fraction (chemistry)","level":2,"score":0.4750088155269623},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.4228825867176056},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3047821819782257},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.254552960395813},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11553364992141724},{"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D009792","descriptor_name":"Oceans and Seas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009792","descriptor_name":"Oceans and Seas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009792","descriptor_name":"Oceans and Seas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009792","descriptor_name":"Oceans and Seas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012623","descriptor_name":"Seawater","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012623","descriptor_name":"Seawater","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012623","descriptor_name":"Seawater","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012623","descriptor_name":"Seawater","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1038/s43588-024-00596-6","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-024-00596-6","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:38413777","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38413777","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":"Nature computational science","raw_type":null},{"id":"pmh:oai:HAL:hal-04489740v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04489740","pdf_url":"https://hal.science/hal-04489740v1/file/2023.05.31.543043v4.full.pdf","source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nature Computational Science, 2024, 4 (2), pp.104-109. &#x27E8;10.1038/s43588-024-00596-6&#x27E9;","raw_type":"Journal articles"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-04489740v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04489740","pdf_url":"https://hal.science/hal-04489740v1/file/2023.05.31.543043v4.full.pdf","source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nature Computational Science, 2024, 4 (2), pp.104-109. &#x27E8;10.1038/s43588-024-00596-6&#x27E9;","raw_type":"Journal articles"},"sustainable_development_goals":[{"score":0.8700000047683716,"display_name":"Life below water","id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G1153485594","display_name":null,"funder_award_id":"A*MIDEX","funder_id":"https://openalex.org/F4320309911","funder_display_name":"Aix-Marseille Universit\u00e9"},{"id":"https://openalex.org/G2689612763","display_name":null,"funder_award_id":"Marie","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3680960908","display_name":null,"funder_award_id":"ANR-19-P3IA-000","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G443217407","display_name":null,"funder_award_id":"PRAIRIE","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G4668103369","display_name":null,"funder_award_id":"AMX-19-IET-01","funder_id":"https://openalex.org/F4320309911","funder_display_name":"Aix-Marseille Universit\u00e9"},{"id":"https://openalex.org/G5280846027","display_name":null,"funder_award_id":"ANR-19-CE45-0008","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G5838787665","display_name":null,"funder_award_id":"ANR-19-P3IA-0001","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G626190807","display_name":null,"funder_award_id":"19-P3IA-0001","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G6697205189","display_name":null,"funder_award_id":"872539","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7303289904","display_name":null,"funder_award_id":"ANR-22-CE45-0007","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7411104504","display_name":null,"funder_award_id":"A*MIDEX","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7440903218","display_name":null,"funder_award_id":"956229","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8318455765","display_name":null,"funder_award_id":"ANR-19","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320306789","display_name":"Ocean Foundation","ror":"https://ror.org/00pw7tr34"},{"id":"https://openalex.org/F4320309911","display_name":"Aix-Marseille Universit\u00e9","ror":"https://ror.org/035xkbk20"},{"id":"https://openalex.org/F4320319437","display_name":"Fondation Tara Oc\u00e9an","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320337386","display_name":"Division of Ocean Sciences","ror":"https://ror.org/05wqqhv83"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392201117.pdf"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W2123845384","https://openalex.org/W2611104626","https://openalex.org/W2775213139","https://openalex.org/W2783336662","https://openalex.org/W2789551594","https://openalex.org/W2792587403","https://openalex.org/W2795247764","https://openalex.org/W2810698935","https://openalex.org/W2884435343","https://openalex.org/W2955167895","https://openalex.org/W2969627863","https://openalex.org/W2979522844","https://openalex.org/W2997994466","https://openalex.org/W3025757981","https://openalex.org/W3047701039","https://openalex.org/W3085875665","https://openalex.org/W3090493712","https://openalex.org/W3113074526","https://openalex.org/W3134677442","https://openalex.org/W3162924116","https://openalex.org/W3216588755","https://openalex.org/W4213139376","https://openalex.org/W4221049439","https://openalex.org/W4226101760","https://openalex.org/W4282939275","https://openalex.org/W4283262943","https://openalex.org/W4284961769","https://openalex.org/W4287993268","https://openalex.org/W4289316047","https://openalex.org/W4321748347","https://openalex.org/W4378783302","https://openalex.org/W4378901396","https://openalex.org/W4382631906","https://openalex.org/W4382632370","https://openalex.org/W6838646446","https://openalex.org/W6887610951","https://openalex.org/W6892469695","https://openalex.org/W6906369916","https://openalex.org/W6911280582","https://openalex.org/W6911361171","https://openalex.org/W6943940698"],"related_works":["https://openalex.org/W2066858118","https://openalex.org/W1976914335","https://openalex.org/W3011699130","https://openalex.org/W2134017072","https://openalex.org/W2915208987","https://openalex.org/W2152256925","https://openalex.org/W1940452713","https://openalex.org/W1994777790","https://openalex.org/W2005567565","https://openalex.org/W2058150833"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
