1,721,011 research outputs found
A ready-to-use database for DADA2: Diat.barcode_rbcL_263bp_DADA2 based on Diat.barcode v9
No full textThis database is an adaptation for DADA2 of Diat.barcode v9. Length of sequences is 263 bp ------------------------- 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/TOMBY
A ready-to-use database for DADA2: Diat.barcode_rbcL_312bp_DADA2 based on Diat.barcode v7
No full textThis 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 version is adapted from Diat.barcode version 7
https://data.inra.fr/dataset.xhtml?persistentId=doi:10.15454/HYRVU
Rsyst::diatom_rbcl_align_312bp database: a database adapted to DNA metabarcoding (version v7: 23-02-2018)
No full textMethod 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
3/ Resulting sequences are dereplicated into Individual Sequence Unit (ISUs) in order to identify taxa sharing identical DNA sequences on the 312bp rbcL barcode region. If necessary, taxonomy is harmonized between all taxa found in each single ISU. Finally, only ISUs are conserved in the database, each represented by 1 taxa ID and DNA sequence.
4/ Resulting ISUs database is assigned to itself using the Mothur assignment algorithm (classify.seqs command). Expected and newly obtained taxonomy are compared to evaluate potential source of biases (erroneous taxonomic name, taxa impossible to differentiate,...). If necessary, ambiguous sequence are removed from the database or taxonomy is adjusted.
5/ Finally, potential conflicting names are harmonized (e.g. "aff." and "cf." removed, "Nanofrustulum_sp._SZCZCH285" transformed into "Nanofrustulum_sp.")
6/ The ".fasta" file contains the rbcL 312bp DNA sequences and the ".txt" file contains the corresponding taxonomy (common sequence ID in both files). The sequence ID is composed by a accession number (present also in R-Syst::diatom library) and a the original taxnomic name given by the author of the sequence (eg: TCC7a-Rbcl-1|Fragilaria_vaucheriae). This sequence ID is shared by the .fasta and .txt files.
7/ The text file gathers the curated taxonomical information from empire to species level. For instance: TCC7a-Rbcl-1|Fragilaria_vaucheriae Eukaryota; Chromista; Chromobiota; Bacillariophyta; Fragilariophyceae; Fragilariales; Fragilariaceae; Fragilaria; Fragilaria_nanoides. In this case, Fragilaria_vaucheriae is the original species name given by the author and Fragilaria_nanoides is the curated species name adapted to metabarcoding.
This database has been curated for a specific use with filtering procedure based on our own experience and is provided on an indicative basis. The original database, R-Syst::diatom, is the reference and you can curate it differently to meet your personal requirements and final usages
Bioindication diatomées : comparaison microscopie / barcoding ADN. Pipeline MOTHUR selectionné
No full textLe pipeline sélectionné pour produire les listes floristiques utilisées pour calculer les IBD des 447 échantillons est donné ci dessou
A ready-to-use database for mothur: Diat.barcode_rbcL_263bp_mothur based on Diat.barcode v9
No full textReady to use database adapted from Diat.barcode v9 for MOTHU
Data supplementing the article “Aquatic biofilms as passive environmental DNA samplers: application to benthic macroinvertebrate communities in rivers” - raw MiSeq data, inventories
No full textThese 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 Ecology Resources” journal.------------------ The directory is composed of: “38_samples_fastq:files”: contains raw demultiplexed fastq files (R1. fastq and R2. fastq) for each of the 38 samples used in this study to produce OTUs and taxonomic inventories.----------------------------- “Samples id.xlsx”: contains the samples ID of the fastq files---------------------------- “Inventories.xlsx”: contains single and multi-habitat morphological inventories as well as molecular inventories resulting from the stud
Bioindication diatomées : comparaison microscopie / barcoding ADN. Données brutes Fastq 2016 + 2017, Test des différentes stratégies bioinfo sur données 2016. Projet AFB numéro 15000239 / A30.
No full textFichiers fastqrassemble 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.xlsxTest des différentes stratégies bioinfo - data 2016.zip>dossier "Free OTU (2016)"
stratégie basée sur les séquences filtrées>dossier "OTU DREAL (2016)"
stratégie basée sur les OTUs, crées soit avec méthode Furthest neighbor ou méthode Opticlust>dossier "Raw_reads (2016)"stratégie basée sur les séquences brute
A ready-to-use database for DADA2: Diat.barcode_rbcL_263bp_DADA2 based on Diat.barcode v12
No full textThis database is an adaptation for DADA2 of Diat.barcode v12. Length of sequences is 263 bp ------------------------- Rimet, Frederic et al., 2018, "Diat.barcode, an open-access barcode library for diatoms", https://doi.org/10.15454/TOMBY
Mayotte rivers: databases used for the development of diatom and macroinvertebrates water quality tools.
No full textDonnées 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 MONNIER et Yorick REYJOL (chargés de mission
A ready-to-use database for DADA2: Diat.barcode_rbcL_263bp_DADA2 based on Diat.barcode v10
No full textThis database is an adaptation for DADA2 of Diat.barcode v10. Length of sequences is 263 bp ------------------------- 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 (2020-11-06
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