search

fbreitwieser / krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
GNU General Public License v3.0
224 stars 43 forks source link

About reference DB #184

Open km-2021 opened 2 months ago

km-2021 commented 2 months ago

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 commented 2 months ago

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.