Contains all the scripts used to perform a 16S analysis to reproduce the results of a study and compare.
WARNING: You MUST have sra-tools installed for this script to run or it will NOT work. Conda environment (with Bioconda) recommended.
Make get_seqs.sh executable and run it inside the folder where your metadata.csv file is located in.
WARNING: You MUST have Docker, Java and Nextflow installed for this script to run or it will NOT work.
Make pipeline_run.sh executable and input the necessary paths. The pipeline should run considering your machine has enough RAM and CPU power.
This R script should generate all the additional plots. It is meant to be used with a slightly formatted beta_diversity file.
These scripts were developed by fonors, goncalof21, MadalenaFranco2 & scmdcunha.