{"id":"https://openalex.org/W7205300413","doi":null,"title":"scRNA-seq with Nanopore sequencing: benchmark of approaches based on hybrid sequencing","display_name":"scRNA-seq with Nanopore sequencing: benchmark of approaches based on hybrid sequencing","publication_year":2022,"publication_date":"2022-07-05","ids":{"openalex":"https://openalex.org/W7205300413"},"language":"en","primary_location":{"id":"pmh:oai:HAL:hal-05144874v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-05144874v1","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://jobim2022.sciencesconf.org/","raw_type":"info:eu-repo/semantics/conferenceObject"},"volume":null,"type":"conference-paper","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal.science/hal-05144874v1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107548700","display_name":"Ali Hamraoui","orcid":"https://orcid.org/0009-0008-7001-4252","observed_orcids":["https://orcid.org/0009-0008-7001-4252"]},"institutions":[{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Hamraoui, Ali","raw_affiliation_strings":["Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)","institution_ids":["https://openalex.org/I29607241","https://openalex.org/I4210129409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083592168","display_name":"Catherine S\u00e9namaud\u2010Beaufort","orcid":"https://orcid.org/0000-0001-7074-0416","observed_orcids":["https://orcid.org/0000-0001-7074-0416"]},"institutions":[{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"S\u00e9namaud-Beaufort, Catherine","raw_affiliation_strings":["Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)","institution_ids":["https://openalex.org/I29607241","https://openalex.org/I4210129409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114635929","display_name":"Audrey Onfroy","orcid":"https://orcid.org/0009-0003-1429-4230","observed_orcids":["https://orcid.org/0009-0003-1429-4230"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Onfroy, Audrey","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052835091","display_name":"St\u00e9phane Le Crom","orcid":"https://orcid.org/0000-0002-0534-7797","observed_orcids":["https://orcid.org/0000-0002-0534-7797"]},"institutions":[{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210097156","display_name":"Biologie Computationnelle, Quantitative et Synth\u00e9tique","ror":"https://ror.org/00pcqj134","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210097156"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Le Crom, St\u00e9phane","raw_affiliation_strings":["Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)","LCQB-GN - Genetic Networks [LCQB] (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)","institution_ids":["https://openalex.org/I29607241","https://openalex.org/I4210129409"]},{"raw_affiliation_string":"LCQB-GN - Genetic Networks [LCQB] (France)","institution_ids":["https://openalex.org/I4210097156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065934968","display_name":"Morgane Thomas\u2010Chollier","orcid":"https://orcid.org/0000-0003-2608-476X","observed_orcids":["https://orcid.org/0000-0003-2608-476X"]},"institutions":[{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Thomas-Chollier, Morgane","raw_affiliation_strings":["Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)","institution_ids":["https://openalex.org/I29607241","https://openalex.org/I4210129409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083286626","display_name":"Laurent Jourdren","orcid":"https://orcid.org/0000-0003-4253-1048","observed_orcids":["https://orcid.org/0000-0003-4253-1048"]},"institutions":[{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jourdren, Laurent","raw_affiliation_strings":["Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)","institution_ids":["https://openalex.org/I29607241","https://openalex.org/I4210129409"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078001342","display_name":"Sophie Lemoine","orcid":"https://orcid.org/0000-0003-0975-5365","observed_orcids":["https://orcid.org/0000-0003-0975-5365"]},"institutions":[{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Lemoine, Sophie","raw_affiliation_strings":["Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomique ENS - GenomiqueENS (GenomiqueENSInstitut de Biologie de l\u2019\u00c9cole normale sup\u00e9rieure - IBENS46, rue d'Ulm75230 Paris Cedex 05France - France)","institution_ids":["https://openalex.org/I29607241","https://openalex.org/I4210129409"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.76063261,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9868000149726868,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9868000149726868,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.012400000356137753,"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/T10885","display_name":"Gene expression and cancer classification","score":9.999999747378752e-05,"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/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.8999999761581421},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"nanopore sequencing","score":0.9020000100135803},{"id":"https://openalex.org/keywords/hybrid-sequencing","display_name":"hybrid sequencing","score":0.7360000014305115},{"id":"https://openalex.org/keywords/long-read-sequencing","display_name":"long-read sequencing","score":0.8500000238418579},{"id":"https://openalex.org/keywords/cell-barcodes","display_name":"cell barcodes","score":0.6480000019073486},{"id":"https://openalex.org/keywords/unique-molecular-identifiers","display_name":"unique molecular identifiers","score":0.8510000109672546},{"id":"https://openalex.org/keywords/flame","display_name":"flames","score":0.9829999804496765},{"id":"https://openalex.org/keywords/promethion","display_name":"PromethION","score":0.7250000238418579},{"id":"https://openalex.org/keywords/oxford-nanopore-minion","display_name":"Oxford Nanopore MinION","score":0.7990000247955322},{"id":"https://openalex.org/keywords/isoform-detection","display_name":"isoform detection","score":0.7889999747276306},{"id":"https://openalex.org/keywords/10x-genomics","display_name":"10x Genomics","score":0.7649999856948853},{"id":"https://openalex.org/keywords/transcriptome-assembly","display_name":"transcriptome assembly","score":0.47099998593330383}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6065999865531921},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6047000288963318},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.4334000051021576},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41130000352859497},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.3767000138759613},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.3061999976634979},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3018999993801117},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2847000062465668},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2799000144004822},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2768999934196472},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.27399998903274536},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.2529999911785126}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:HAL:hal-05144874v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-05144874v1","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://jobim2022.sciencesconf.org/","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-05144874v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-05144874v1","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://jobim2022.sciencesconf.org/","raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3158466915","https://openalex.org/W4414003366","https://openalex.org/W7008217214","https://openalex.org/W4413271628","https://openalex.org/W7167468400","https://openalex.org/W4362666539","https://openalex.org/W3177450887","https://openalex.org/W7135218338","https://openalex.org/W3048389895","https://openalex.org/W7128649220"],"abstract_inverted_index":{"Long-read":[0],"sequencing":[1,9,57,111,316,372,398],"has":[2],"recently":[3],"been":[4,87],"incorporated":[5],"into":[6],"single-cell":[7,303,415],"RNA":[8,384,405],"studies.":[10],"Compared":[11],"tothe":[12],"standard":[13],"Illumina":[14,99,159,214],"short-read":[15],"library":[16],"that":[17,176,310],"primarily":[18],"captures":[19],"abundance":[20],"information,":[21],"Nanopore":[22,47,96,315,368,401],"sequencinghas":[23],"several":[24,32,83],"advantages":[25],":":[26],"it":[27,35,64,240],"can":[28],"produce":[29],"reads":[30,97,196],"of":[31,95,105,136,185,190,229,246,314,360,414],"kb":[33],"[1],":[34],"provides":[36],"more":[37,195],"precise":[38],"transcriptomemapping/assembly":[39],"and":[40,71,119,132,149,181,420],"detects":[41],"complex":[42],"isoform":[43,266,273],"variants.In":[44],"the":[45,54,68,93,106,125,134,137,150,154,163,171,218,255,284,311,320,331,339,345,358,400],"10xGenomics":[46],"data":[48,230],"analysis,":[49],"a":[50,102,141,147,226],"key":[51],"challenge":[52],"is":[53,263,281],"relatively":[55],"low":[56],"accuracy":[58,317],"(~95%":[59],"per":[60],"base)":[61],"which":[62],"makes":[63],"difficult":[65],"to":[66,91,139,166,208,213,282,290,298],"detect":[67],"cell":[69,370],"barcodes":[70],"UMI":[72,203],"information":[73],"in":[74,183,287,302,357,386,418],"each":[75,288],"Nanoporeread":[76],"[1].":[77],"To":[78],"deal":[79],"with":[80,158,277,403,422],"this":[81],"issue,":[82],"bioinformatics":[84],"approaches":[85],"have":[86],"developed":[88],"using":[89,98,305],"hybridsequencing":[90],"guide":[92],"allocation":[94],"data.We":[100],"performed":[101],"benchmark":[103],"analysis":[104],"available":[107],"Single-Cell":[108],"long-read":[109,361,423],"hybrid":[110,306],"basedpipelines:":[112],"Sicelore":[113,198,221],"[2],":[114],"Snuupy":[115,177,191,233],"[3],":[116],"Scnapbar":[117,182],"[4],":[118],"Flames":[120,180,253],"[5].":[121],"We":[122,308],"first":[123],"compared":[124,157],"performance":[126,224],"ofeach":[127],"pipeline":[128,138,289,297],"for":[129,265],"barcode-UMI":[130],"detection":[131,274],"assignment,":[133],"ability":[135],"handle":[140],"large":[142,227],"set":[143,228],"ofdata":[144],"sequenced":[145],"on":[146,199,254,399],"PromethION,":[148],"biological":[151,168,210],"results":[152,169,174,211,250],"at":[153,170,217],"gene":[155,219],"level":[156],"results.We":[160],"then":[161],"selected":[162],"best":[164,285],"tools":[165],"compare":[167],"transcript":[172,300],"level.Our":[173],"showed":[175,222],"outperforms":[178],"Sicelore,":[179],"terms":[184],"barcode-UMIassignment.":[186],"The":[187,249],"polyA-independant":[188],"algorithm":[189],"assigns":[192],"around":[193],"35%":[194],"than":[197],"aMinION":[200],"dataset.":[201],"This":[202],"count":[204],"increase":[205],"allows":[206],"us":[207],"obtain":[209],"closer":[212],"resultsthan":[215],"sicelore":[216],"level.":[220],"good":[223],"processing":[225],"fromPromethION":[231],"where":[232],"could":[234],"not":[235,259],"achieve":[236],"its":[237,247,272],"process,":[238],"suggesting":[239],"cannot":[241],"be":[242],"used":[243],"without":[244],"importantmodifications":[245],"code.":[248],"produced":[251],"by":[252,330,344],"assignment":[256],"part":[257],"were":[258],"convincing":[260],"but":[261],"asit":[262],"designed":[264],"detection,":[267],"we":[268],"are":[269],"now":[270],"testing":[271],"module":[275],"coupled":[276],"Siceloreand":[278],"Snuupy.Our":[279],"aim":[280],"select":[283],"features":[286],"ultimately":[291],"develop":[292],"an":[293],"optimal,":[294],"scalable":[295],"andreproducible":[296],"characterize":[299],"isoforms":[301,417],"data,":[304],"sequencing.":[307,424],"alsoforesee":[309],"announced":[312],"improvement":[313],"may":[318],"leverage":[319],"need":[321],"ofIllumina":[322],"sequencing.AcknowledgementsThe":[323],"IBENS":[324],"genomics":[325],"core":[326],"facility":[327],"was":[328],"supported":[329],"France":[332],"G\u00e9nomique":[333],"national":[334],"infrastructure,":[335],"funded":[336],"as":[337],"partof":[338],"\u201cInvestissements":[340],"d'Avenir\u201d":[341],"program":[342],"managed":[343],"Agence":[346],"Nationale":[347],"de":[348],"la":[349],"Recherche":[350],"(contract":[351],"ANR-10-INBS-09).References1.":[352],"Full":[353],"article:":[354],"Single-cell":[355,396],"transcriptomics":[356],"context":[359],"nanopore":[362],"sequencing.https://www.tandfonline.com/doi/full/10.1080/13102818.2021.1988868.2.":[363],"High":[364],"throughput":[365],"error":[366],"corrected":[367],"single":[369],"transcriptome":[371,397],"|":[373],"Nature":[374],"Communications.https://www.nature.com/articles/s41467-020-17800-6.3.":[375],"Long,":[376],"Y.":[377],"et":[378,394,410],"al.":[379,395,411],"FlsnRNA-seq:":[380],"protoplasting-free":[381],"full-length":[382,416],"single-nucleus":[383],"profiling":[385],"plants.":[387],"Genome":[388,425],"Biol.22,":[389],"66":[390],"(2021).4.":[391],"Wang,":[392],"Q.":[393],"platform":[402],"ScNapBar.":[404],"27,":[406],"763\u2013770(2021).5.":[407],"Tian,":[408],"L.":[409],"Comprehensive":[412],"characterization":[413],"human":[419],"mouse":[421],"Biol.":[426],"22,":[427],"310":[428],"(2021).":[429]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-09-02T00:00:00"}