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PanExplorer_workflow

Prerequisites - Tool dependencies

  • Snakemake
  • Roary
  • PGAP
  • Panaroo
  • ncbi-blast+
  • R

Install

1- Git clone

git clone https://github.com/SouthGreenPlatform/PanExplorer_workflow.git

2- Define the PANEX_PATH environnement variable

cp -rf PanExplorer_workflow /usr/local/bin
export PANEX_PATH=/usr/local/bin/PanExplorer_workflow

3- Get preformatted RPS-BLAST+ database of the CDD COG distribution

wget https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/little_endian/Cog_LE.tar.gz
tar -xzvf Cog_LE.tar.gz
cp -rf Cog.* $PANEX_PATH/COG

Prepare your list of genomes to be analyzed

Edit a new file names "genbank_ids" listing the Genbank identifiers of complete assembled and annotated genomes. The file should look like this

cat genbank_ids
CP000235.1
CP001079.1
CP001759.1
CP015994.2

Run the workflow

Creating a pangenome using Roary

snakemake --cores 1 -s $PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG

Creating a pangenome using PanACoTA

snakemake --cores 1 -s $PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG

Creating a pangenome using PGAP

snakemake --cores 1 -s $PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG