R scripts and data processing pipeline for: Comparing DNA Extraction Protocols for Freshwater Prokaryotic Communities: Impacts on Yield and Microbial Profiling

This repository contains the complete analytical pipeline and datasets supporting the study on DNA extraction protocol optimization for freshwater microbial ecology. The objective is to ensure full transparency and reproducibility of the results Contents: Scripts: Complete R workflow, including the DADA2 pipeline (processing raw FASTQ files to ASV tables) and downstream analysis scripts (numbered 01-08) for composition, alpha/beta diversity, core community analysis, and differential abundance. Data: Raw DADA2 outputs (seqtab.nochim.rds, taxarc.rds). Cleaned and intermediate Phyloseq objects (ps_tree.rds, ps_filtre_rare_rel_all.rds). Metadata and physical measurement files (metadata.csv, plot_dna_quantity.csv, rapport_abs.csv). Helper Files: fonction.R containing custom plotting and data cleaning functions. Instructions: To reproduce the analysis, please refer to the README.txt file included in the repository for script sequencing and required R packages.