Database indexes for Kraken and Kraken2

I want to try using Kraken or Kraken2 on one of my datasets, but I can se that Kraken has no database, and Kraken2 doesn’t have one for bacteria. Is there any way to add databases to a program, or to request an addition to a database?

Kind regards, Line

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Hi @Line_HK!

Sorry for the delay, the Galaxy EU has been undergoing many changes.

The Kraken tool already has indexes added at Galaxy Main, so using the tool there is an alternative for now. Galaxy AU is also a choice. Both include Bacteria.

The Kraken tool could have indexes added at Galaxy EU. The administrators would need to make that decision. Ping @hxr @bjoern.gruening @wm75

The Kraken2 tool suite is currently having the associated Data Manager updated (a tool that installs the indexes). It is not quite ready to be used yet, and probably is why you don’t see those indexes at the EU server now.

Kraken2 is not installed at Main or AU yet (primary tools or DM), but I expect that we will add it/create indexes at Main once the DM is ready for use. Not sure about AU, @Slugger70 can comment more if he wants, but I would expect about the same answer.

Please feel free to ask for an update in about a month if you don’t see the indexes/tool versions updated at these public servers.


Update: The Kraken2 data manager was just released today. Please give it a test run if you still want to use it:

We’ll be adding the full Kraken2 tool suite to Galaxy Main soon, with indexes, if all works out as planned. Expect other usegalaxy.* servers will do the same.

I updated the kraken2 databases on Hope that is useful!


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Is there a way to load the pre-build SILVA database provided from Kraken2? (if not in, than in local galaxy)

EDIT: I found it in the Special DB :slight_smile:



I am looking for a way to upload or create a Kraken2 custom build index of desired sequence from NCBI in Galaxy EU Is it possible to do so?

Thank you in advance for your reply!