Data and code : Coastal rocky reef fish monitoring in the context of the Marine Strategy Framework Directive: environmental DNA metabarcoding complements underwater visual census

Info : This repository includes the data and R scripts used for the analyses and figures of the submitted article "Rey et al. (2022) - Coastal rocky reef fish monitoring in the context of the Marine Strategy Framework Directive: environmental DNA metabarcoding complements underwater visual census." Contact : anais.rey47@hotmail.fr and pierre.thiriet@mnhn.fr Contents : This repository contains the raw data, metadata and scripts used to process the data of this paper. 01_Demultiplexing : This folder contains raw data from sequencing, metadata and scripts used to demultiplex raw reads, remove primers and prepare samples for the DADA2 pipeline. 02_DADA2_TaxonomicAssignment : This folder contains metadata, reference databases and scripts used to run the DADA2 pipeline to make ASVs and assign the ASVs with RDP Classifier, BLAST and ECOTAG. 03_Post_ASVs_processing : This folder contains (1) the ASV tables for 12S and 16S and their taxonomic assignment with RDP Classifier, BLAST and ECOTAG (2) the R script used to process the ASVs (index jumping filtering, LULU, ...), to make the final choice of taxonomic assignment and the clustering of ASVs into OTU with SWARM. This script prepares the OTU tables for 12S and 16S which will be used for the statistical analyses (3) the data (ex. LULU outputs, SWARM outputs, ...) and metadata needed to process the script. 04_Statistical_analyses : This folder contains (1) the R scripts performing the statistical analyses and comparing UVC and eDNA metabarcoding diversity data (2) the data (ex UVC data) and metadata needed to process the script