I have a question about the q2-picrust2 version which you commit on Jan 23, 2020 [For QIIME2 Ver 2019.10]. What is the placement tool that is being used: is it the default EPA-NG? Because the q2-picrust2 plug-in did not have an input for this parameter.
I checked that in later versions you updated the placement tool option, but in the version I am using (2019.10), there is no such option in the _full_pipeline.py. So, I am a bit confused in why this is so. If you can please help me, that would be great. I should mention that I got all the outputs (KO, EC, Pathway), so the analysis worked well.
Yes, prior to the most recent release (earlier this month) the only placement tool you could run with PICRUSt2 directly was EPA-NG, so that’s what it must have been.
In general environmental samples will be harder to predict because microbes in those samples are often highly dissimilar to existing reference genomes. That being said, I would use EPA-NG over SEPP if you have sufficient computational resources.
