# Project: Comparison of DNA Extraction Methods for Freshwater Microbial Communities
# Author: Arthur Szylit
# Date: 2026-01-29

## OVERVIEW
This repository contains all R scripts and data necessary to reproduce the findings of the study. 
The analysis pipeline follows the logical order numbered from 01 to 08.

## DIRECTORY STRUCTURE
- /scripts: Contains 8 R scripts for data processing, statistics, and figure generation.
- /data: Contains raw data (seqtab, taxarc), metadata, and intermediate phyloseq objects (.rds).
- fonction.R: Custom R functions used across multiple scripts.

## DATA DESCRIPTION
- seqtab.nochim.rds & taxarc.rds: Outputs from the DADA2 pipeline.
- metadata.csv: Sample information (Protocol codes, brand, sampling site).
- plot_dna_quantity.csv & rapport_abs.csv: DNA yield and quality (NanoDrop) measurements.
- ps_tree.rds: Final phyloseq object including the phylogenetic tree.

## INSTRUCTIONS
1. Set the working directory to the root of this unzipped folder.
2. Ensure the following R packages are installed: phyloseq, vegan, ggplot2, dplyr, patchwork, ANCOMBC,
3. Run scripts in sequential order (01 to 08). 
   - Scripts 01-02: Data formation and normalization.
   - Scripts 03-04: Analysis of DNA yield and alpha diversity and absorbance (Figures 1, 2, 3,4).
   - Scripts 05-08: Community composition, core taxa, and differential abundance (Figures 5 and supplementary).

## SOFTWARE VERSIONS
- R version: 4.3.3
- Key packages: phyloseq (1.46.0), vegan (2.6-4), ANCOMBC (2.4.0).