This repository countains the code of the bioinformatics pipelines used in the manuscript "Alterations in the composition and function of the gut microbiota are associated with COVID-19 and its severity in North African and European populations", Bredon M et al.

This directory contains files for processing paired-end shotgun metagenomic reads using Snakemake.

Example command to run Snakemake on the cluster:

snakemake --cluster "qsub -q beta -l select=1:ncpus=12 -l walltime=10:00:00 -N Snakemake -m bea" --jobs 20 -s 1-0.Clean_data --keep-going

Data Cleaning & Assembly

1-0.Clean_data: This first step is essential for the rest of the pipeline. Using raw reads, this script cleans the reads and removes human contaminants.

1-1 Snakefile_Assembly: This script is used to build the metagenomes, predict the ORFs and check the number of reads used for assembly.

Taxonomic & Functional annotation of reads

2-0.Snakefile_Kraken: Taxonomic annotation using Kraken.

2-1.Snakefile_Metaphlan: Taxonomic annotation using Metaphlan4.

2-2.Snakefile_Humann: Functional annotation using HUMAnN 3.0.

Taxonomic & Functional annotation of contigs

3-0.Snakefile_Diamond: Annotation using Diamond & Megan.

3-1.Snakefile_CAT-BAT: Annotation using CAT-BAT.

3-2.Snakefile_dbcan2: CAZyme annotation using dbcan2.