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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

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.

Please note: the documentation is undergoing a rewrite! There will be more advanced topics added soon. The original readme is copied at the end of this page, and sections from it are being removed as new pages are added to this wiki.

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 my_sample_name 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 SAMPLE tb --output out.json --format json --seq 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

Citation

Hunt M, Bradley P, Lapierre SG et al. Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe [version 1; peer review: 2 approved, 1 approved with reservations]. Wellcome Open Res 2019, 4:191 (https://doi.org/10.12688/wellcomeopenres.15603.1)

Please cite us if you use Mykrobe predictor in a publication.

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The original README is below, but each section of it will gradually be replaced as the documentation is reorganised.

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Table of Contents generated with DocToc

• Mykrobe
• Citation
• Tests
• Release

Mykrobe

http://www.mykrobe.com

Citing

If you use one of the following panels please cite the relevant publications:

mykrobe predict tb_sample_id  tb --panel walker-2015 -1 tb_sequence.bam

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 15.10 (2015): 1193-1202.

mykrobe predict tb_sample_id  tb --panel bradley-2015 -1 tb_sequence.bam

Bradley, Phelim, et al. "Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis." Nature communications 6 (2015).

Tests

To run tests:

Requires mongod. Download.

mongod

and in another window.

  pip install tox
  tox

To run tests for a particular python version run, e.g. python 3.6:

tox -e py36

Release

See dist/README.md