I’m running a metagenomics workflow on Galaxy and have reached the functional annotation step using DIAMOND.
Currently, the only databases available in the DIAMOND tool are RefSeq and UniProtKB/Swiss-Prot.
For compatibility with HUMAnN, I need to use the UniRef90 database for protein family annotation.
Could you please let me know if UniRef90 is available on this Galaxy instance, or if it can be added to the DIAMOND database options?
They said “If your database of interest is not listed, contact your Galaxy admin”, so I guess something can be done. Anyone knows who is the Galaxy admin in this case?
Which Galaxy server are you working at? The server URL please – find this at the top of your browser window. Thanks!
Then, if you would like to move over to a UseGalaxy server, most will have the UniRef90 database already included. Screenshot from the UseGalaxy.eu server.
If you are following this GTN tutorial, how to check which servers will support the tools/data is in the Available at these Galaxies menu at the top. The EU server is probably the best choice since that is where the scientists who developed the workflow are working but any should be fine while learning.
Who to contact to install new reference data will vary by server and there are ways to connect to most the indexes hosted at public servers though a shared resources. We can help you to find the administrators and let them know.
My issue is that I’m trying to perform an assembly-based functional annotation — starting from scaffolds, not from raw reads, from my metagenomic sequencing.
The workflow I was following is: Prodigal (gene prediction) → DIAMOND (protein annotation using UniRef90 database) → HUMAnN (metabolic pathway reconstruction) → UniRef to KEGG KO conversion.
The problem is that I cannot find the UniRef90 database among the available reference databases in the DIAMOND tool on Galaxy.
I understand that a read-based profiling directly with HUMAnN is simpler, but since I already have assembled scaffolds, I would like to perform a more targeted assembly-based analysis.
Could you please tell me if the UniRef90 database can be made available for DIAMOND on Galaxy Europe, or who I should contact to request it?
Yes, I understood your request but was hoping to alert about some of the details involved. I’m not sure if your planned route through these tools is going to produce the result you want. All three analysis paths involve abundance calculations, and interpretations. But I’m guessing that you know this and want to try anyway!
