myco 
myco is group of pipelines built for phylogenic analysis of the Mycobacterium tuberculosis complex (MBTC). It builds upon existing tools such as clockwork and UShER to accomplish this task.
Which workflow should I use?
Each version of myco is relatively similar. Where they differ is the sort of the inputs they expect. In all cases, your FASTQs must be paired-end Illumina reads.
This is a companion discussion topic for the original entry at github.com/aofarrel/myco/myco_cleaned