Running Kraken2 on GTDB

Question

[Nazifa Ahmed]

Hi,

Can anyone tell me how to use a GTDB as the reference database for Kraken2? A step by step guide would be very helpful. Thank you!

[shenwei356]

I've got one: https://github.com/shenwei356/kmcp/tree/main/benchmarks#custom-database-for-kraken-and-bracken

Note that the kraken2 database with GTDB r202 would be more than 200GB.