Functional Analysis Using EMU Output – Has Anyone Tried This?

Question

[henrique.mouradias]

Hi everyone,

Has anyone here tried performing functional analysis using outputs from the EMU pipeline (for 16S taxonomy assignment)? I’m particularly interested in linking EMU's species-level taxonomy to predicted functions (e.g., metabolic pathways).

What tools or pipeline did you use for this? Any tips or workflow suggestions would be really appreciated.

Thanks in advance!

Answer 1

[andres.firrincieli]

You can't use EMU with tools like PICRUSt2 because it doesn't produce typical outputs such as OTUs or ASVs. EMU works more like a read-level classifier to compute species abundances.

For long-read 16S rRNA metabarcoding, you need a pipeline that provides representative sequences for each species, eg LACA (https://www.biorxiv.org/content/10.1101/2023.11.26.568539v1)