Main tool : Mykrobe
Full documentation: https://github.com/Mykrobe-tools/mykrobe/wiki
This docker image was created with the intention of analyses involved with Mycobacterium tuberculosis and other similar Mycobacterium species, so genotyphi and sonneityping are not included in this image.
The docker image for Mykrobe was built on 2023-11-08, and thus contains the most recent database that was available at the time.
### OUTPUT FROM mykrobe panels describe run on 2023-11-08: ###
$ mykrobe panels describe
#0 12.57 Gathering data from /usr/local/lib/python3.9/site-packages/mykrobe/data
#0 12.57
#0 12.57 Species summary:
#0 12.57
#0 12.57 Species Update_available Installed_version Installed_url Latest_version Latest_url
#0 12.57 sonnei no 20210201 https://ndownloader.figshare.com/files/26274424 20210201 https://ndownloader.figshare.com/files/26274424
#0 12.57 staph no 20201001 https://ndownloader.figshare.com/files/24914930 20201001 https://ndownloader.figshare.com/files/24914930
#0 12.57 tb no 20230928 https://figshare.com/ndownloader/files/42494211 20230928 https://figshare.com/ndownloader/files/42494211
#0 12.57 typhi no 20221208 https://ndownloader.figshare.com/files/38478086 20221208 https://ndownloader.figshare.com/files/38478086
#0 12.57
#0 12.57 sonnei default panel: 20210201
#0 12.57 sonnei panels:
#0 12.57 Panel Reference Description
#0 12.57 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
#0 12.57 20210201 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 (same as 20201012, but with lineage3.7.30 added)
#0 12.57
#0 12.57 staph default panel: 20170217
#0 12.57 staph panels:
#0 12.57 Panel Reference Description
#0 12.57 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)
#0 12.57
#0 12.57 tb default panel: 202309
#0 12.57 tb panels:
#0 12.57 Panel Reference Description
#0 12.57 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
#0 12.57 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
#0 12.57 202206 NC_000962.3 AMR panel '202010' combined with the WHO 2021 catalogue (doi:10/h298 and doi:10/h299), and lineage scheme from Chiner-Oms 2020
#0 12.57 202309 NC_000962.3 AMR panel '202010' combined with the WHO 2021 catalogue (doi:10/h298 and doi:10/h299), lineage scheme from Chiner-Oms 2020, and updated species based on GTDB r214 (doi:10.1093/nar/gkab776)
#0 12.57 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)
#0 12.57 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 - 1202mykrobe predict -s SAMPLE -S tb -o out.json --format json -i test_reads.fq.gz