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Built in Panels
This page describes the panels included with mykrobe, and the command mykrobe panels.
After installing mykrobe, run:
mykrobe panels update_metadata
mykrobe panels update_species all
and you will have the built-in panels installed and can use them with mykrobe predict.
Keep reading if you want to know more details...
At the time or writing, mykrobe supports AMR calling for Mycobacterium tuberculosis, Staphylococcus aureus, and Shigella sonnei. The panel data are not included in with the source code. They must be downloaded after installation. Mykrobe allows for panel data updates without needing to install the code again.
Run these two commands to get (or update) all supported panels:
mykrobe panels update_metadata
mykrobe panels update_species all
The panel files are by default stored in the same location where mykrobe itself is installed. This location can be changed using the option --panels_dir (this option is available for all mykrobe panels commands and when running mykrobe predict). For ease of use it is recommended to use the default, unless for some reason this is not possible.
Example putting the panel data in a directory called panel_data:
mykrobe panels --panel_dir panel_data update_metadata
mykrobe panels --panel_dir panel_data update_species all
Obtain information on the currently installed panels by running:
mykrobe panels describe
If no panels are installed, the output will look like this:
Gathering data from /your/install/directory/mykrobe/data
No data
If panels are available, but not installed (ie you ran mykrobe panels update_metadata only) the output will look like this:
Gathering data from /your/install/directory/mykrobe/data
Species summary:
Species Update_available Installed_version Installed_url Latest_version Latest_url
sonnei yes None NA 20201012 https://ndownloader.figshare.com/files/25038821
staph yes None NA 20201001 https://ndownloader.figshare.com/files/24914930
tb yes None NA 20201014 https://ndownloader.figshare.com/files/25103438
No panels are installed
Running mykrobe panels update_species all will install all available updates. Then the output of mykrobe panels describe will look something like this:
Gathering data from /your/install/directory/mykrobe/data
Species summary:
Species Update_available Installed_version Installed_url Latest_version Latest_url
sonnei no 20201012 https://ndownloader.figshare.com/files/25038821 20201012 https://ndownloader.figshare.com/files/25038821
staph no 20201001 https://ndownloader.figshare.com/files/24914930 20201001 https://ndownloader.figshare.com/files/24914930
tb no 20201014 https://ndownloader.figshare.com/files/25103438 20201014 https://ndownloader.figshare.com/files/25103438
sonnei default panel: 20201012
sonnei panels:
Panel Reference Description
20201012 NC_016822.1 Genotyping panel for Shigella sonnei based on scheme defined in Hawkey 2020, and panel for variants in the quinolone resistance determining regions in gyrA and parC
staph default panel: 20170217
staph panels:
Panel Reference Description
20170217 BX571856.1 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 default panel: 202010
tb panels:
Panel Reference Description
201901 NC_000962.3 AMR panel based on first line drugs from NEJM-2018 variants (DOI 10.1056/NEJMoa1800474), and second line drugs from Walker 2015 panel
202010 NC_000962.3 AMR panel based on first line drugs from NEJM-2018 variants (DOI 10.1056/NEJMoa1800474), second line drugs from Walker 2015 panel, and lineage scheme from Chiner-Oms 2020
bradley-2015 NC_000962.3 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)
walker-2015 NC_000962.3 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
We recommend to run mykrobe predict using the default panel (in fact for sonnei and staph there is currently only one panel). For tb there is a choice of several panels. To run predict using a different panel, use the --panel option, for example to use the older walker-2015 panel instead of the default panel 202010, run:
mykrobe predict --sample sample_name --species tb --panel walker-2015 --seq reads.fastq