Quickstart - picrust/picrust2 GitHub Wiki

If you just want to get started... this is just the basics.

Install PICRUSt2

Install it in its own environment and then activate this:

mamba create -n picrust2 -c bioconda -c conda-forge picrust2=2.6.1
mamba activate picrust2

If you need more instructions, see the installation page.

Run PICRUSt2

You will need:

1. A fasta file containing the ASVs (or other representative sequences) from your study
2. A feature table in either BIOM or tsv format that contains the abundance of each sequence within each sample (sequences should be rows, samples should be columns)

Run PICRUSt2 full pipeline:

picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1

-p is the number of threads that you'll be using.

You can see the full details for running PICRUSt2 here.