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1 to 10 of 11 Results
May 25, 2020
Rimet, Frederic; Chonova, Teofana; Gassiole, Gilles; Gusev, Evgenuy; Kahlert, Maria; Keck, François; Kelly, Martyn; Kulikovskiy, Maxim; Maltsev, Yevhen; Mann, David; Pfannkuchen, Martin; Trobajo, Rosa; Vasselon, Valentin; Wetzel, Carlos; Zimmermann, Jonas; Bouchez, Agnès, 2018, "Diat.barcode, an open-access barcode library for diatoms", https://doi.org/10.15454/TOMBYZ, Portail Data INRAE, V7
Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems, and...
Feb 24, 2020
Rivera, Sinziana; Vasselon, Valentin; Mary, Nathalie; Monnier, Olivier; Rimet, Frédéric; Bouchez, Agnès, 2020, "Data supplementing the article “Aquatic biofilms as passive environmental DNA samplers: application to benthic macroinvertebrate communities in rivers” - raw MiSeq data, inventories", https://doi.org/10.15454/SXKA8I, Portail Data INRAE, V2, UNF:6:qkDWkBPhUOQHwccJmQL5Ng== [fileUNF]
These data supplement the article “Aquatic biofilms as passive environmental DNA samplers: application to benthic macroinvertebrate communities in rivers” Sinziana F. Rivera, Valentin Vasselon, Nathalie Mary, Olivier Monnier, Fréderic Rimet & Agnès Bouchez submitted to “Molecular...
Feb 24, 2020
Rivera, Sinziana; Vasselon, Valentin; May, Nathalie; Monnier, Olivier; Rimet, Frédéric; Bouchez, Agnès, 2020, "Data supplementing the article “Aquatic biofilms as passive environmental DNA samplers: application to benthic macroinvertebrate communities in rivers” - Macroinvertebrate reference library", https://doi.org/10.15454/UNUFWY, Portail Data INRAE, V1
These data supplement the article “Aquatic biofilms as passive environmental DNA samplers: application to benthic macroinvertebrate communities in rivers” Sinziana F. Rivera, Valentin Vasselon, Nathalie Mary, Olivier Monnier, Fréderic Rimet & Agnès Bouchez submitted to “Molecular...
Sep 25, 2019
Rimet, Frédéric; Tapolczai, Kalman; Vasselon, Valentin; Mary, Nathalie; Bouchez, Agnès, 2019, "Mayotte rivers: databases used for the development of diatom and macroinvertebrates water quality tools.", https://doi.org/10.15454/6Z5IAH, Portail Data INRAE, V1, UNF:6:ONruidDb0OPOqJ6sI38KPQ== [fileUNF]
Données ayant servi au projet "Développement d’outils de bio-indication «phytobenthos» et «macro-invertébrés benthiques» pour les eaux de surface continentales de Mayotte". Ce projet a été financé par l'AFB, Agence Française pour la Biodiversité Les correspondants AFB: Olivier MO...
Jul 19, 2019 - CARRTEL Dataverse
Rimet, Frederic; Bouchez, Agnès, 2019, "Life-forms, cell-sizes and ecological guilds of diatoms in European rivers", https://doi.org/10.15454/XLQ40G, Portail Data Inra, V1
Diatoms are a very diverse group of microalgae that encompass about 100 000 taxa. This makes an excellent bioindicator especially of rivers. The majority of biotic indices based on diatoms are constructed on species pollution-sensitivities. Nevertheless, recent studies showed the...
Mar 5, 2019
Rivera, Sinziana; Vasselon, Valentin; Chardon, Cécile; Jacas, Louis; Guéguen, Julie; Bouchez, Agnès; Rimet, Frédéric, 2019, "Bioindication diatomées : comparaison microscopie / barcoding ADN. Pipeline MOTHUR selectionné", https://doi.org/10.15454/1OTGWL, Portail Data INRAE, V1, UNF:6:ajEMExtsrc4xeT8GdJzfgQ== [fileUNF]
Le pipeline sélectionné pour produire les listes floristiques utilisées pour calculer les IBD des 447 échantillon est donné ci dessous
Mar 5, 2019 - CARRTEL Dataverse
Keck, François; Rimet, Frédéric; Vasselon, Valentin; Bouchez, Agnès, 2019, "A ready-to-use database for DADA2: Diat.barcode_rbcL_312bp_DADA2", https://doi.org/10.15454/HNI1EK, Portail Data Inra, V1
This database is an adaptation for DADA2 of : Vasselon, Valentin; Rimet, Frederic; Bouchez, Agnès, 2018, "Rsyst::diatom_rbcl_align_312bp database: a database adapted to DNA metabarcoding (version v7: 23-02-2018)", https://doi.org/10.15454/HYRVUH, Portail Data Inra, V1 This versio...
Dec 4, 2018
Rivera, Sinziana; Vasselon, Valentin; Chardon, Cécile; Guéguen, Julie; Bouchez, Agnès; Rimet, Frédéric, 2018, "Bioindication diatomées : comparaison microscopie / barcoding ADN. Données brutes Fastq 2016 + 2017, Test des différentes stratégies bioinfo sur données 2016. Projet AFB numéro 15000239 / A30.", https://doi.org/10.15454/9EG5Z4, Portail Data INRAE, V1, UNF:6:ajEMExtsrc4xeT8GdJzfgQ== [fileUNF]
Fichiers fastq rassemble tous les fichier fastq des échantillons de 2016 et 2017 Ils sont numérotés de 1.fastq à 464.fastq La correspondance avec les échantillons est donné dans le fichier Suivi_Mothur_Run_Dreal_2016_2017.xlsx Test des différentes stratégies bioinfo - data 2016.z...
Dec 4, 2018
Rivera, Sinziana; Vasselon, Valentin; Chardon, Cécile; Jacas, Louis; Guéguen, Julie; Bouchez, Agnès; Rimet, Frederic, 2018, "Bioindication diatomées : comparaison microscopie / barcoding ADN. Listes floristiques, indices IBD. Projet AFB numéro 15000239 / A30.", https://doi.org/10.15454/WNI6FQ, Portail Data INRAE, V1
Description des 3 fichiers excels : DREAL 2016_2017 liste taxonomique microscopie_moleculaire.xlsx : Fichier excel donnant les listes floristiques diatomées des campagnes 2016 et 2017 obtenues. 3 onglets : - "Microscopie" : listes obtenues en microscopie optique -"Moleculaire" :...
Aug 10, 2018
Vasselon, Valentin; Rimet, Frederic; Bouchez, Agnès, 2018, "Rsyst::diatom_rbcl_align_312bp database: a database adapted to DNA metabarcoding (version v7: 23-02-2018)", https://doi.org/10.15454/HYRVUH, Portail Data INRAE, V1
Method followed to obtain the Rsyst::diatom_rbcl_align_312bp database: 1/ Extraction of the 312bp rbcL barcode from the full Rsyst::diatom database rbcL alignment (using Diat_rbcL_108F and R3 primers). 2/ Sequences with ambiguities (N), homopolymers > 8 and length < 312bp are rem...
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