BAGA genome analysis pipeline for recombination

Script to run a comparative genomics analysis pipeline using the Bacterial and Archaeal Genome Analyser. This analysis infers homologous recombination rates in two sets of samples of Pseudomonas aeruginosa from cystic fibrosis chromic airway infection sputum samples. This script succesfully completed on a Debian Linux computer with 12GB memory and 100sGB disk space. If you have trouble using baga raise an issue at https://github.com/daveuu/baga or email: david.williams@liverpool.ac.uk. The VCFs and multiple sequence alignments produced are available at DOIs: 10.6084/m9.figshare.1521307 and 10.6084/m9.figshare.1521131