RE: PICRUSt2 reference KEGG Database

[nazarGL (Nazar Mo)]

PICRUSt2 reference KEGG Database

Hi @Faisal, There isn't a tutorial yet, but you can see what the required alignment/tree files look like here: https://github.com/picrust/picrust2/wiki/Sequence-placement#using-custom-reference-files You can take a look at those and also the default gene family abundance tables, which are also packaged in the picrust2 github repo. Best, Gavin

Hi
can you help, please by the exact workflow-commands to run q2-PICRUSt2 for fungal ITS data?
Thank you.

[gmdouglas (Gavin Douglas)]

Hi there,

The q2-picrust2 plugin is just for the default 16S pipeline. You can run ITS with the standalone version (see: Frequently Asked Questions · picrust/picrust2 Wiki · GitHub), but I don't recommend this for standard analyses because the predictions are very low accuracy.

Best,

Gavin

[nazarGL (Nazar Mo)]

Thank you for your reply

[Mehrbod_Estaki]

Hi @nazarGL,
Though not really the same thing as what PICRUTS2 does for 16S predictions, you may be interested in checking out the FUNguild tool/paper if you are trying to extract functional information from your fungi data. Note I have never used it myself, just passing on info.