Main tool : Mykrobe
Additional tools:
- genotyphi 2.0
- sonneityping v20210201
- python 3.10.6
- biopython 1.79
- pandas
Full documentation: https://github.com/Mykrobe-tools/mykrobe/wiki
This docker image was created with the intention of running genotyphi on FASTQ files from Salmonella Typhi isolates using the Mykrobe implementation of genotyphi. However, this docker image contains the full (bio)conda environment for mykrobe, and thus can be used for other organisms as well (Mycobacterium tuberculosis, Staphylococcus aureus, Shigella sonnei)
The docker image was also created with the intention of running Mykrobe on Shigella sonnei FASTQ files, and therefore includes the python script from sonneityping which can be used to parse the outputs of mykrobe.
The docker image for Mykrobe was built on 2022-11-02, and thus contains the most recent database that was available at the time.
### OUTPUT FROM mykrobe panels describe run on 2022-11-02: ###
$ mykrobe panels describe
# Species summary:
# Species Update_available Installed_version Installed_url Latest_version Latest_url
# 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 20220705 https://ndownloader.figshare.com/files/36197349 20220705 https://ndownloader.figshare.com/files/36197349
# typhi no 20210323 https://ndownloader.figshare.com/files/28533549 20210323 https://ndownloader.figshare.com/files/28533549
# sonnei default panel: 20210201
# 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
# 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)
# 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: 202206
# 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
# 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
# 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
# typhi default panel: 20210323
# typhi panels:
# Panel Reference Description
# 20210323 AL513382.1 GenoTyphi genotyping scheme and AMR calling using Wong et al 2016 (https://doi.org/10.1038/ncomms12827) and updates as described in Dyson & Holt 2021 (https://doi.org/10.1101/2021.04.28.441766)Following directions from here for running the mykrobe implementation of genotyphi: https://github.com/katholt/genotyphi#running-mykrobe
# launch the container interactively
$ docker run --rm -v $PWD:/data -u $(id -u):$(id -g) -it staphb/mykrobe:0.12.1
# run genotyphi/mykrobe on Illumina reads from a Salmonella typhi isolate
$ mykrobe predict --sample SRR3277297 --species typhi --format json --out SRR3277297.genotyphi.json --seq SRR3277297_1.fastq.gz SRR3277297_2.fastq.gz
# parse mykrobe output with helper script from genotyphi; generate TSV
$ python /genotyphi/parse_typhi_mykrobe.py --jsons SRR3277297.genotyphi.json --prefix mykrobe_out
SRR3277297
# print out results TSV
$ column -t -s, -n mykrobe_out_predictResults.tsv
genome species spp_percent final genotype confidence acrB_R717L acrB_R717Q num QRDR lowest support for genotype marker poorly supported markers max support for additional markers additional markers node support parC_S80R parC_S80I parC_E84G parC_E84K gyrA_S83F gyrA_S83Y gyrA_D87G gyrA_D87N gyrA_D87V gyrA_D87Y gyrB_S464F gyrB_S464Y catA1 dfrA7 sul1 sul2 strA strB mphA TEM1 qnrS1 ermB CTXM15 tetB tetA dfrA5 dfrA15 IncFIAHI1 IncHI1A IncHI1BR27 IncHI1_ST6 IncY z66
SRR3277297 typhi 91.715 2.3.1 strong 0 0 1 1 (1; 0/69); 2 (1; 0/102); 2.2 (1; 134/0); 2.3 (1; 110/0); 2.3.2 (1; 82/0); 2.3.1 (1; 106/0) 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0# launch the container interactively
$ docker run --rm -v $PWD:/data -u $(id -u):$(id -g) -it staphb/mykrobe:0.12.1
# run genotyphi/mykrobe on Illumina reads from a Salmonella typhi isolate
$ mykrobe predict --sample Ssonnei --species sonnei --format json_and_csv --out Ssonnei --seq shigella_sonnei_R1.fastq.gz shigella_sonnei.fastq.gz
# parse mykrobe output JSON with helper script from sonneityping; must use alleles.txt file found inside docker container
# generate TSV output
$ python /sonneityping/parse_mykrobe_predict.py --jsons Ssonnei.json --alleles /sonneityping/alleles.txt --prefix sonneitypping-results
# print out results TSV
$ column -t -s $'\t' -n sonneitypping-results.tsv
genome species final genotype name confidence num QRDR parC_S80I gyrA_S83L gyrA_S83A gyrA_D87G gyrA_D87N gyrA_D87Y lowest support for genotype marker poorly supported markers max support for additional markers additional markers node support
Ssonnei S. sonnei 3.6.1.1.2 CipR.MSM5 strong 3 1 1 0 1 0 0 lineage3 (1; 65/0); lineage3.6 (1; 94/0); lineage3.6.1 (1; 59/0); lineage3.6.1.1 (1; 74/0); lineage3.6.1.1.2 (1; 65/0)