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Mykrobe

http://www.mykrobe.com

The following help pages are available:

• Installation instructions
• Information on built-in variant panels for mykrobe predict
• How to run AMR prediction (the most common use of mykrobe)
• An explanation of the output from running AMR prediction
• How to cite mykrobe

Advanced topics:

• How to use custom variant panels
• How to do custom lineage calling
• How to genotype a list of variants and/or presence of sequences (no AMR or lineage calling)
• If you made your own panel and have a problem with missed calls: use background variants in your panel.

Quick start

Install

• bioconda - conda install -c bioconda mykrobe
• from source - pip3 install . && mykrobe panels update_metadata && mykrobe panels update_species all
• or using singularity or docker (see wiki for details)

Run AMR prediction

Run on Mtb, making a JSON file of results:

mykrobe predict --sample my_sample_name \
  --species tb \
  --output out.json \
  --format json \
  --seq reads.fq.gz

Test on example data

You can test that mykrobe predict runs as expected by downloading and running on a small toy set of reads, as follows.

wget -O test_reads.fq.gz https://ndownloader.figshare.com/files/21059229
mykrobe predict -s SAMPLE -S tb -o out.json --format json -i test_reads.fq.gz

The test reads are simulated, and perfectly match the reference, except for the isoniazid resistant associated variant inhA I21T. You should see a section like this in the output file out.json:

"Isoniazid": {
    "predict": "R",
    "called_by": {
        "inhA_I21T-ATC1674262ACT": {
    ... etc