90a96749-8fa1-467d-9af8-bd4ab1ae48bd Desdouits Marion IFREMER 04 67 13 04 14 Station de Palavas - Chemin de Maguelone - 34250 Palavas les Flots Station de Palavas - Chemin de Maguelone - 34250 Palavas les Flots Palavas France France marion.desdouits@ifremer.fr pointOfContact 2025-12-14T12:56:27.404273Z ISO 19115-3 - SEXTANT ISO 19115-3 - SEXTANT 1.0 0 WGS 84 (EPSG:4326) EPSG 8.6 SARS-CoV-2 whole genome sequencing in wastewaters SARS-CoV-2 whole genome sequencing in wastewaters Séquençage SARS-CoV-2 dans les eaux usées - Obépine 2021-01-01 creation 2022-02-02 publication FR-330-715-368-00032-IFR_BIOINFO_SEQ_SARS_OBEPINE DOI:10.12770/90a96749-8fa1-467d-9af8-bd4ab1ae48bd WGS of SARS-CoV-2 by Oxford Nanopore Technology from raw wastewater samples collected in France, 2020-2021 Ifremer - Laboratoire Sante Environnement Microbiologie IFREMER sismer@ifremer.fr publisher Barbe Laure Laboratoire de Microbiologie, LSEM, Ifremer. 02 40 37 43 33 Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03 Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03 Nantes France France Laure.Barbe@ifremer.fr author Schaeffer Julien Laboratoire de Microbiologie, LSEM, Ifremer. Julien.Schaeffer@ifremer.fr author Besnard Alban Laboratoire de Microbiologie, LSEM, Ifremer. Alban.Besnard@ifremer.fr author Jousse Sarah Laboratoire de Microbiologie, LSEM, Ifremer. Sarah.Jousse@ifremer.fr author Scientific interest group Obépine author Françoise S Le Guyader Laboratoire de Microbiologie, LSEM, Ifremer. author Desdouits Marion Laboratoire de Microbiologie, LSEM, Ifremer. marion.desdouits@ifremer.fr author https://sextant.ifremer.fr/geonetwork/srv/api/records/90a96749-8fa1-467d-9af8-bd4ab1ae48bd/attachments/BioinfoMarine.png Habitats and biotopes Habitats and biotopes Habitats et biotopes GEMET - INSPIRE themes, version 1.0 GEMET - INSPIRE themes, version 1.0 2018-07-27T14:39:48 publication 2018-07-27 publication geonetwork.thesaurus.external.theme.httpinspireeceuropaeutheme-theme /Biological Environment/Bioinformatics /Biological Environment/Bioinformatics /Milieu biologique/Bio-Informatique Thèmes Sextant Thèmes Sextant 2025-12-09 publication geonetwork.thesaurus.local.theme.sextant-theme Variables ODATIS Variables ODATIS 2023-10-13 publication geonetwork.thesaurus.local.theme.odatis_variables Bioinformatics Bioinformatics Bioinformatique ODATIS aggregation parameters and Essential Variable names ODATIS aggregation parameters and Essential Variable names 2025-07-29 publication geonetwork.thesaurus.external.theme.NVS.OD1 Analysis data Analysis data Données d'analyse Type de jeux de donnée ODATIS Type de jeux de donnée ODATIS 2025-12-09 publication geonetwork.thesaurus.local.theme.type_jeux_donnee CC-BY (Creative Commons - Attribution) CC-BY (Creative Commons - Attribution) CC-BY (Creative Commons - Attribution) grid utf8 -6.00 11.932 40.9268 51.20 2021-01-01 2021-12-31 /home/ref-bioinfo/ifremer/obepine /home/ref-bioinfo/ifremer/obepine NETWORK:LINK https://data-dataref.ifremer.fr/bioinfo/ifremer/obepine/lsem/ https://data-dataref.ifremer.fr/bioinfo/ifremer/obepine/lsem/ WWW:DOWNLOAD Lien de téléchargement Lien de téléchargement Lien de téléchargement https://doi.org/10.12770/90a96749-8fa1-467d-9af8-bd4ab1ae48bd https://doi.org/10.12770/90a96749-8fa1-467d-9af8-bd4ab1ae48bd DOI Digital Object Identifier (DOI) Raw wastewaters (WW) were collected weekly from two WW treatment plants in a city in western France. A subsample was ultracentrifuged, nucleic acids axtracted from the pellet, RNA reverse-transcribed and submitted to an optimized ARTIC400 V3 PCR. PCR products were purified, barcoded and adapter-ligated using Oxford Nanopore Technology kits, and libraries sequenced on an R9.4 flow cells using a Mk1c MinION. Results from 6 runs are shared as raw data (fast5 files) and based-called data using Guppy 4.3.4 (fastq files).