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:

shopt -s expand_aliases


Instructions for using Pilon can be found on the Pilon Wiki

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