is it rational to compare/align our local WGS tub sequences with all available tuberculosis WGS strains?
I have aligned all our 165 samples with the Cole`s 1998 WGS tuberculosis strain. All SNPs are found OK. Now I want to choose the other reference files. I could find 29 of them. Are there more and are they all suitable for comparing our local samples?
And should I align against a set of references or group them somehow in NextGene software?