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Built in Panels
This page describes the panels included with mykrobe, and the command mykrobe panels.
For the origin of each built in panel, and links to the publications, please see the citing mykrobe page.
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, Shigella sonnei, Salmonella enterica serotype Paratyphi B, and Salmonella Typhi. 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
paratyphiB yes None NA 20230627 https://figshare.com/ndownloader/files/43870968
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
typhi yes None NA 20221208 https://ndownloader.figshare.com/files/38478086
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
paratyphiB no 20230627 https://figshare.com/ndownloader/files/43870968 20230627 https://figshare.com/ndownloader/files/43870968
sonnei no 20210201 https://ndownloader.figshare.com/files/26274424 20210201 https://ndownloader.figshare.com/files/26274424
staph no 20201001 https://ndownloader.figshare.com/files/24914930 20201001 https://ndownloader.figshare.com/files/24914930
tb no 20230928 https://figshare.com/ndownloader/files/42494211 20230928 https://figshare.com/ndownloader/files/42494211
typhi no 20221208 https://ndownloader.figshare.com/files/38478086 20221208 https://ndownloader.figshare.com/files/38478086
paratyphiB default panel: 20230627
paratyphiB panels:
Panel Reference Description
20230627 CIP54_115 Genotyping scheme for Salmonella enterica serovar Paratphi B PG1
... and then descriptions of the other species ...
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