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README.md

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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
  1. 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
  1. Run Prokka to get Roary compatible features files
snakemake _all_prokka
  1. 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