Awesome

Mykrobe

Antibiotic resistance prediction in minutes.

Currently supports Mycobacterium tuberculosis, Staphylococcus aureus, Shigella sonnei, Salmonella typhi and Salmonella enterica serotype Paratyphi B.

http://www.mykrobe.com

Documentation

Please see the mykrobe wiki for documentation. For S. typhi also see https://github.com/katholt/genotyphi

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 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

(It is possible to output most of the results as CSV, but some information is lost (does not fit easily in tabular/csv format)

Test reads can be obtained by running:

wget -O reads.fq.gz https://ndownloader.figshare.com/files/21059229