Diag pipeline

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Basic usage

With Docker

Whithout Docker

Setup reference data

Core genome

VFDB database

Advanced usage

change snp caller

perform snp calling complete genome

perform snp calling on other reference than the pre-defined reference

use custom virulence database

Dev

Take example of

https://github.com/pnnl/hundo/blob/master/hundo/scripts/build_report.py

https://pnnl.github.io/hundo/

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