This repository contains the analysis code and metadata of the paper "Seasonal dynamics are the major driver of microbial diversity and composition in intensive freshwater aquaculture" doi:
data - contains the output files from the dada2 workflow and the metadata for each sample scripts - additional code that is implemented throughout the analysis tables - intermediate output data tables
'Dor_16S_dada2_preprocess.R' - preprocessing of teh dada2 output for further statistical analyses 'Dor_alpha_div.R' - Alpha diversity analysis 'Dor_aqua_pred_lm.R' - aquaculture related regression models 'Dor_beta_div.R' - Beta diversity analysis 'Dor_cyanos.R' - analysis of cyanobacteiral sequences 'Dor_enrichments.R' - sequence enrichment analyses 'Dor_env_par.R' - RDAs 'Dor_unique_species.R' - unique and shared ASVs between samples