Antibiotic resistance prediction in minutes.
Currently supports Mycobacterium tuberculosis, Staphylococcus aureus, Shigella sonnei, Salmonella typhi and Salmonella enterica serotype Paratyphi B.
Please see the mykrobe wiki for documentation. For S. typhi also see https://github.com/katholt/genotyphi
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