Data from the Aquaref 2024 project : Microscopy/DNA inventories and Diatoms Biological Index (IBD) lists

These data were generated as part of the Aquaref 2014 project for the assessment of the Diatoms Biological Index (IBD) required by the Water Framework Directive (WFD). The objective of this project is to establish a methodological framework that links molecular and morphological indices, using microscopy as the reference method. An R-based gateway was developed in three parts, using data collected from diatom sampling campaigns DREAL 2016-17, DREAL Bretagne 2019, MetaIBD 2021-22 and Aquaref 2024 projects. Bioinformatic analyses were performed on FastQ files using the DADA2 pipeline. The resulting output files (ASV table and taxonomy table) were then used to develop the R-based gateway using the following scripts : Pre-SEEE script : Transforms DNA data (DADA2 output files) and corrects read abundances using CFv3. Post-SEEE script (transformation) : Processes and reformats the SEEE output files. Post-SEEE script (linear model) : Applies the linear model to adjust the SEEE results. This directory contains the following files : Microscopy_species_inventories_2016-2022.csv: Contains counts of cells identified through microscopy of 2016 to 2022 samples. Microscopy_species_inventories_2024.csv: Contains counts of cells identified through microscopy of 2024 samples. DNA_species_inventories.csv: Includes read abundance results obtained after the CFv3 correction (output file from the pre-SEEE R script). IBD_DNA_results_before_model.csv: Lists IBD results for DNA data after SEEE calculation, prior to correction using the linear model. Corrected_IBD_DNA_results.csv: Lists IBD results for DNA data after SEEE calculation, following correction with the linear model (Corrected_IBD_CFv3_model). IBD_microscopy_results_2016-22.csv: Contains IBD results for microscopy data from 2016 to 2022 after SEEE calculation. IBD_microscopy_results_2024.csv: Contains IBD results for microscopy 2024 data after SEEE calculation. Files are also available in format .xlsx : Microscopy_species_inventories_2016-2022.xlsx Microscopy_species_inventories_2024.xlsx DNA_species_inventories.xlsx IBD_DNA_results_before_model.xlsx Corrected_IBD_DNA_results.xlsx IBD_microscopy_results_2016-22.xlsx IBD_microscopy_results_2024.xlsx.