MethanoReplica is a project dedicated to replicating and validating the results of the study "Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand."
- Download original Bioproject files into fastq;
- Generates:
- bi-clustered heatmap;
- scatter plot of OTUs abundance vs prevalence
- barplot of relative taxonomy composition at Phylum level for each sample
- PCoA graph.
# Download the project
wget https://github.com/Rendrick27/MethanoReplica/archive/refs/heads/main.zip
# Unzip the folder
unzip main.zip# Navigate to the directory
cd main.zip- process_metadata.sh -> Downloads the Bioproject in fastq files with the following formart
DNA_dreid_irrigated_rep1_R1.fastq.gz
#This script must be runned in the main folder- diversity_mapper_PCoA.py -> Creates a PCoA graph based on results from the nextflow pipeline (It requires the beta-diversity.97.summary file)
#This script must be runned in folder of results>postprocessing- run_pipeline.sh -> Runs the nextflow pipeline
#This script must be runned in folder of nextflow
GPLv3