Please see the mykrobe wiki for documentation.
Install:
- bioconda -
conda install -c bioconda mykrobe - from source -
pip3 install . - or using singularity or docker (see wiki for details)
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 reads can be obtained by running:
wget -O reads.fq.gz https://ndownloader.figshare.com/files/21059229