New preprint: comparing different genetics analysis pipelines for tuberculosis

Ruan Spies has done a careful systematic comparison of the current genetics pipelines that purport to take raw genetic reads from a clinical sample containing M. tuberculosis (or Mycobacteria generally) and process them to produce a putative genome from which an antibiogram can be predicted. He couldn't get some of the pipelines to work but of the others, with a few exceptions, AMR prediction performance was often similar. The non-functional features of EIT Pathogena stand-out; these are things like resilience, ease-of-use, speed and security. You can read about it here.