Mykrobe

Mykrobe can be used on Staphylococcus aureus and Mycobacterium tuberculosis samples only. Predictions are based directly on the fastq reads. Version 0.5.6 is used.

Parameters

For M. tuberculosis, two different panels of mutations can be analysed, by defining the variable mykrobe_panel. Two different values are possible:

• bradley-2015, from Bradley et al. 2015, Nature Communications (default value)
• walker-2015, from Walker et al. 2015, Lancet Infectious Diseases

The threshold of confidence for Mykrobe can also be defined with mykrobe_confidence. The default value is 10.