Approaches to functional profile assessment


#1

Hello,

I’m assessing some 16S data from soil samples. QIIME2 gave me everything I wanted and more for my taxonomic comparisons, but I’m looking to compare functional profiles of my treatments.

What is your preferred method to take the standard QIIME2 outputs and view them through a functional perspective? Someone recommended PICRUSt, but it looks like the plugin for that hasn’t been completed. Are there alternatives, or is that my best bet?

Ideally, the solution wouldn’t be computationally intensive – the government shutdown is preventing my access to computational resources. I am stuck using my regular laptop for now.

Thanks you,
Matt


(Matthew Ryan Dillon) #2

Have you seen this? https://library.qiime2.org/plugins/q2-picrust2/13/


#3

I ran into that before, but had trouble when I saw that the plugin utilized a different version of greengenes. I’ll have to see if my regular laptop has the computational capacity to retrain my data with the version used in PICRUSt.

Thank you for the link.