Quick Start

## Quick Start (included in example.bash) ``` $ cat example.bash # generate pan-genome prediction using PEPPA python PEPPA.py -P examples/GCF_000010485.combined.gff.gz –min_cds 60 –incompleteCDS s -p examples/ST131 examples/*.gff.gz

# generate summaries for PEPPA predicted CDSs and pseudogenes python PEPPA_parser.py -g examples/ST131.PEPPA.gff -s examples/PEPPA_out -m -t -c -a 95

# generate summaries for PEPPA predicted CDSs only python PEPPA_parser.py -g examples/ST131.PEPPA.gff -s examples/PEPPA_out -m -t -c -a 95 -P ```