Installation

1. Clone this directory and PanPhlAn into a local folder:

git clone https://github.com/zhaoc1/pangenome-snakemake.git my_pangenome_project
cd my_pangenome_project
hg clone https://bitbucket.org/CibioCM/panphlan local/panphlan

2. Creat a new Conda environment (assumes you have Miniconda)

conda create -n my_pan --file=conda-requirements.txt --quiet --yes

Annotating genomes

1. Manually doanload reference genomes and clean up names

snakemake clean_names

2. Run Prokka to get Roary compatible features files

snakemake _all_prokka

3. Collect GFF files into gffs/

mkdir prokka_gffs
cp fnas/prokka_*/*.gff prokka_gffs

Creating the pangenome using Roary

snakemake run_roary

Visualizing Roary results

snakemake visualize_roary