Creating a custom trait table

This page is currently a work in progress, but I aim to provide some instructions on how you can add a trait or traits of interest to a custom trait table.

The basic steps here are to:

1. Download the GTDB reference genomes (r214.1) (gtdb_genomes_reps_r214.tar.gz in here)
2. Filter these genomes to only those included within PICRUSt2 (i.e. the genomes in default files: archaea/archaea_metadata.csv and bacteria/bacteria_metadata.csv)
3. Annotate the genomes with your function of interest
4. Count the number of copies of this function within each genome
5. Create a table containing these counts for each of the bacteria and archaea

Before starting, you will need either:

• A method for annotating the genomes with your function of interest
• A file containing gene sequences for proteins known to carry out the function that you are interested in

I will give instructions for creating a Hidden Markov Model with the gene sequences and applying this to all of the PICRUSt2 genomes.