Request to enable KEGG and Pfam databases for DRAM Annotate on Galaxy Europe

[german_coy_lopez]

Hello,

I am using the DRAM Annotate tool on Galaxy Europe for my metabolic analyses. Currently, I can only select UniRef and VOGDB in the annotation options. However, I also need KEGG and Pfam annotations to obtain complete functional results and to proceed successfully with DRAM Distill.

Could you please enable the KEGG and Pfam databases for DRAM Annotate, or let me know if there is a way to access these options on the server?

Thank you very much for your help!

[jennaj]

Welcome @german_coy_lopez

We have an open request for this but it is still pending and some of it is unlikely to be completed on the public servers due to licensing reasons.

@jennaj

Yes, for now you will need to supply your own reference data for the tool to use (from the history, as described in the guide I linked).

For the native index choices, we are still waiting for this request to be processed:

@jennaj

Now, while you can supply your own annotation files, it would be nicer to have the native indexes. I’ve requested this at → Request: add native indexes for the DRAM suite of tools · Issue #1562 · usegalaxy-eu/infrastructure-playbook · GitHub

Hope this helps to clarify the status! I could get the annotation tool to run correctly (see my original testing history linked above – some test are in the hidden tab) but the data is incomplete with the current limited native indexes.

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For metagenomic analysis, this is the current tool many are using. This annotates the reads, not assemblies, based on abundance information.

• HUMAnN to profile presence/absence and abundance of microbial pathways and gene families
• GTN tutorials for HUMAnN

More tools you can explore:

• PfamScan search a FASTA sequence against a library of Pfam HMM
• Get Pathways Look up KEGG pathways for given Ensembl transcripts
• gProfiler Convert converts between various types of namespaces
• AnnotateMyIDs annotate a generic set of identifiers

For KEGG and assemblies, we had a related discussion about this last week.

• Diamond UniRef90 - #3 by elena.peresani

Some of the complications are rooted in the KEGG data not being a public database. Anyone can use the public Galaxy servers .. but if a dataset or tool is restricted to academics or requires a commercial license, hosting by public Galaxy servers isn’t possible.

• KEGG FTP Academic Subscription

I hope this helps to explain the situation!