How can I import an existing Bracken database into QIIME2?

[ehdud0505 (Doyoung Jin)]

Dear qiime2 teams,

Hi everyone,

My professor has already installed a Kraken2 database on our server, so I am trying to use the existing database instead of building a new one with kraken2-build provided by the QIIME2 mosh plugin.

I was able to import the Kraken2 database into QIIME2 without any issues.
However, I cannot import the Bracken database — QIIME2 doesn’t seem to recognize the format, and there is no direct importer available.

Is there any way to import an existing Bracken database into QIIME2?
Or does the mosh plugin require that Bracken databases must be generated using its own build workflow?

Any advice or workaround would be greatly appreciated!

Thanks in advance.

Best regards,

[ebolyen (Evan Bolyen)]

Hello @ehdud0505,

You should be able to import it as a directory if the files resemble this RegEx:

database(\d{2,})mers\.kmer_distrib$

You'll just use a standard import command with the type set to BrackenDB

qiime tools import \
  --input-path <your database directory> \
  --output-path db.qza \
  --type 'BrackenDB'

[ehdud0505 (Doyoung Jin)]

Hi, @ebolyen ,

It's working now.

Thank you so much for your help — I really appreciate it!

Best Regards,