Kraken database from the CARD Antibiotic Resistance Database

These scripts

1. Download the antibiotic resistance genes and ontology from the Comprehensive Antibiotic Resistance Database
2. Create a taxonomy based on the ontology file
3. 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.

Usage

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 .

Testing

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