Running Kraken2 on GTDB

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!

genome kraken2 gtdb annotation database taxonomy

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updated 4.3 years ago by shenwei356

• written 4.3 years ago by Nazifa Ahmed •

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.

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written 4.3 years ago by shenwei356

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