Picrust2 and metagenomic contributions

[Marco Constante]

Hi all,

I was wondering whether there is a way to have the metagenomic contributions per bacteria/OTUs/SNVs with Picrust2 (It was done with metagenomic_contributions.py in Picrust 1).

I would like to know which bacteria are responsible for a given function.

Thanks!

Marco

[Gavin Douglas]

Hi there,

In PICRUSt2 you will want to generate the stratified output to see these contributions. This will create a table with columns for both functions (e.g. KOs, ECs, pathways) and sequences (i.e. ASVs) along with the abundance within each sample. This stratified output will be produced when the --stratified option is set with picrust2_pipeline.py. Note that this option can result in very high memory usage depending on the number of ASVs and samples due to the huge tables that can result.

Best,

Gavin

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[Alli Weis]

Hi Gavin, 

Would I be able to use that ' --stratified' option in qiime2 plugin of picrust2, or just with the standalone?   How would you do it using the qiime2 full pipeline command? I'm also interested in which bacteria are responsible for the differentially abundant pathways. 

thanks, 

Alli

[Gavin Douglas]

Hi there,

The stratified output is only implemented in the standalone version currently.

Gavin

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