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Mykrobe-tools / mykrobe

Antibiotic resistance prediction in minutes
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resistance database #61

Closed cytang19 closed 5 years ago

cytang19 commented 5 years ago

Hi, how do I use different version of panel? (ex. walker-2015 has 2017 version and 2019 version, by default 2019 version is used but I want to use the 2017 version). Also, can you explain what is the difference between the two versions? What is updated? Thanks.

mbhall88 commented 5 years ago

There is actually a subcommand of mykrobe you can run to get this information: mykrobe panels

$ mykrobe panels
species panel-name  description
tb  bradley-2015    AMR panel described in Bradley, P et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat. Commun. 6:10063 doi: 10.1038/ncomms10063 (2015).
tb  walker-2015 AMR panel described in Walker, Timothy M et al. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. The Lancet Infectious Diseases , Volume 15 , Issue 10 , 1193 - 1202
tb  201901  AMR panel based on first line drugs from NEJM-2018 variants (DOI 10.1056/NEJMoa1800474), and second line drugs from Walker 2015 panel.
staph   default AMR panel described in Bradley, P et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat. Commun. 6:10063 doi: 10.1038/ncomms10063 (2015).

A manuscript is currently in preparation to evaluate and describe the 2019 panel. Stay tuned!