This repository contains all scripts etc. related to the master thesis project:
Exploring the impact of CRISPR-Cas and anti-CRISPR on host-virus interactions in Pseudomonas aeruginosa - Large-scale genomic analysis in the context of human phage therapy (June 2020, Master of Bioinformatics at KU Leuven university)
This project consisted first of the assembly of around 600 in-house sequenced isolates. Next, these were complemented with 4812 genomes issued from the NCBI repository and the whole dataset was then annotated for CRISPR-Cas and anti-CRISPR presence. Both of these steps are implemented in a Snakemake workflow. Finally, several sets of infectivity data to Pseudomonas phages were integrated and statistical analyses were conducted to find the influence of CRISPR-Cas and anti-CRISPR on the genome size and susceptibility of a P. aeruginosa strain.
In addition to a folder per aforementioned stage, a markdown file with other used commands is available.