Running Picrust 2.6.0 or later (Picrust2-SC db) from qiime2?

[matti.r...@gmail.com]

Hi,

Is it possible to install a version of Picrust2 with the recently updated SC database to run the tool as a qiime2 plugin? Currently it seems that the latest one is 2.5.3 (https://github.com/picrust/q2-picrust2/blob/master/environment-files/q2-picrust2-qiime2-amplicon-2024.5.yml). I'm not sure about all the dependencies, or how the standalone Picrust2 is linked to qiime2, but it seems like just updating the version number here doesn't cut it. 

Any ideas? Or should I just give up and run the 2.6.0 (or 2.6.2) as a standalone through export and import back to my qiime2 pipeline?

With Best Regards,

Matti Ruuskanen

[Robyn Wright]

Hi there,

Unfortunately I haven't updated PICRUSt2 for QIIME2 yet - I have been working on it but still have a few things to work out to get it running there. For now it's only possible to use the new database with the standalone PICRUSt2. 

I hope that I will have that done before too long, but I'm preparing for a few other things at the moment so am not actively working on it. 

Robyn

[Jayalal Kj]

Hi,-

I am currently working with Mothur (v1.48.0) for salmon gut microbiota analysis (16S V3–V4 dataset).

Could you please share the complete set of Mothur commands or script you used to generate the output files? Specifically, I would like to understand the steps for generating the key output files used in your analysis.

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[Jayalal Kj]

HI again,

I am currently working with Mothur (v1.48.0) to analyse a 16s V3–V4 dataset from salmon gut microbiota. I am interested in utilising PICRUSt2 for functional prediction based on my Mothur outputs.

Could you please share the complete set of PICRUSt2 commands or scripts required to process Mothur output files? Specifically, I would like to understand the steps involved in generating the key output files used in your analysis.

[Robyn Wright]

Hi Jay,

I haven't personally used Mothur for a while so I can't share a set of scripts, but I don't think you will need much anyway. All you need for running PICRUSt2 is a fasta file of your sequences and either a BIOM file or a tab-delimited feature table containing counts of your sequences within your samples (I think this is what the shared file is within Mothur). You can take a look at the files in this zipped folder to see what these should look like. Note that you don't need the metadata file. You can then just run the full pipeline script using these. 

Robyn

[matti.r...@gmail.com]

Hi,

Thanks for the info, Robyn! For now I'll run 2.6.2 separately from Qiime2.

Best,

Matti

[Robyn Wright]

OK great. Just an FYI that if you used conda/mamba to install before today, some of the default reference files will be missing. For some reason it updated some of the new version for itself, but not all of it. It should be fixed as of a few hours ago, but I'm currently installing/testing it. 

Robyn