Build Kraken2 database using GTDB 16s sequences

DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system

MIT License

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Build Kraken2 database using GTDB 16s sequences #302

Open HitMonk opened 4 years ago

HitMonk commented 4 years ago

Hello, I was wondering if anyone had built a Kraken2 database using GTDB 16s sequences? I have managed to build Kraken2 databases using whole genome GTDB sequences through Struo, however that doesnt work with 16s sequences. Would be grateful if you have suggestions on how i can go about doing this.

jenniferlu717 commented 4 years ago

We only have included compatibility for the 16S Greengenes, SILVA, and RDP databases currently. You can make a database for the 16S GTDB sequences if you can format the taxonomy to contain the correct nodes.dmp/names.dmp files. If you contact those working with the GTDB databases, they might be able to help you there.