Running picrust on shotgun output from bracken

[Håkon Kaspersen]

Dear authors,
I was wondering if picrust2 was solely for 16S data, or if it is possible to run it on Bracken/BIOM outputs from shotgun data as well?
I want to do a simple functional analysis of the identified taxa in the dataset, can this be done with picrust2?

Thanks in advance!

[Robyn Wright]

Hello,

If you have shotgun data then I would recommend running something that identifies the functions that are in your reads, rather than predicting based on taxonomy. The simplest tool for this is probably HUMAnN3 (see here), but we also have a tutorial for using MMSeqs2 here. Also note that if your samples are not human, you may not get such good results with HUMAnN3.

Best wishes,
Robyn

[Håkon Kaspersen]

Thank you for the feedback! I'll have a look at MMSeqs2 since I am not working with human samples.