About reference DB

[km-2021]

I created two different databases, one with Bacteria+Virus and another with Bacteria+Fungi+Virus, and ran them, resulting in slightly different outcomes. Would it be more accurate to create and run separate reference databases for Bacteria, Virus, and Fungi when using Krakenuniq to get more precise results?

[salzberg]

In general it should be more accurate to create 1 DB with all the organisms you're looking for, and just run KrakenUniq once. If a read has a better match to a fungus than to a bacterium, then in your setup it will report different matches in the 2 runs.