An updated update to the pipeline for pangenome investigation. This branch ONLY works for finding EXACT protein variants, and should ONLY be run with parameters as follows:
panaroo -i <your_gff_files> -o <out_dir>
--clean-mode strict
--threshold 1.0
--family_threshold 1.0
--len_dif_percent 1.0
--family_len_dif_percent 1.0
--refind-mode off
--merge_paralogs (optional, but how I use it)
--remove-invalid-genes
-t <threads>
git clone https://github.com/LijMeh/panaroo_ucf.git
cd panaroo_ucf
pip install -e .
Additional dependencies can be installed from the environment panaroo_for_git.yml
mamba env create -f panaroo_for_git.yml
Documentation for Panaroo can be found here