These scripts
- Download the antibiotic resistance genes and ontology from the Comprehensive Antibiotic Resistance Database
- Create a taxonomy based on the ontology file
- Update the sequences such that the new taxonomy IDs
Note that when either a ontology term has multiple parents, or a sequence is assigned to more than one term, one is arbitrarily taken.
The repository already contains the processed library/ and taxonomy/ files - so you can go ahead and run
kraken-build --build --db .
If you would like to start from scratch, run
make clean
make
kraken-build --build --db .
To test the new database, you can try re-classifying the library sequences
kraken --db . library/* > test.kraken
kraken-report --db . > test.report
(c) Florian Breitwieser, 2015