autoMLST2 is free and open-source with no login requirement. It can also be used as a stand-alone application:
Click the links below to download the reference database:
Follow these steps to set up and run the AutoMLST2 stand-alone version on your local unix-based machine:
AutoMLST2_standalone/
AutoMLST2_standalone/automlst2/
Bacteria_db.zip
), extract it, and move the entire resulting Bacteria_db/
folder into:AutoMLST2_standalone/automlst2/
cd AutoMLST2_standalone/automlst2/
docker-compose build --no-cache
uploads
directory and place your genome files there:AutoMLST2_standalone/uploads/job_input/
job_output
). It will be created automatically in:AutoMLST2_standalone/results/
/absolute/path/to/AutoMLST2_standalone/
with your actual path):
docker run --rm -it \
-v /absolute/path/to/AutoMLST2_standalone/uploads:/uploads \
-v /absolute/path/to/AutoMLST2_standalone/results:/results \
-v ./Bacteria_db:/app/Bacteria_db:ro \
-v ./filtered_hmm.LIB:/app/filtered_hmm.LIB:ro \
automlst2_backend \
/uploads/job_input /results/job_output
docker run automlst2_backend --help
Note: The analysis results will be available in the output folder specified. The final tree can be found at results/job_output/final.tree
.