From the Pilon documentation:
"Pilon uses read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies as well as call variants."
To run this software interactively in a Linux environment use the commands:
module load pilon pilon [options]
Because this software uses an alias for to create the pilon command, to use this software in a PBS script you will need to add the following line to your script before loading the pilon module:
Instructions for using Pilon can be found on the Pilon Wiki