Pathogen outbreak study - Pseudomonas single isolate WGS

SNP analysis is done with freebayes (on quality trimmed and filtered reads) with default settings ( -C 2 -min_coverage 0) after which consensus fastas are built against the reference genome for P.aerug. These consensus fastas are fed to kSNP3 along with the reference genome for SNP calling and phylogenetic tree building. I ran a test of a small subset of samples (/ceph/cbio/users/katie/Nicol/Ps_small_test on Ilifu) to test the effect of different coverage cutoffs, including -C 10 and there was no change in the resulting kSNP3 phylogenetic tree structure. Freebayes uses information across all samples (bayesian approach) to call samples, making it robust to low coverage bases