# pilon

## Summary

+ **Module Name:** pilon
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [https://github.com/broadinstitute/pilon/wiki](https://github.com/broadinstitute/pilon/wiki)

## Software Description

From the Pilon documentation: \"Pilon uses read alignment analysis to
diagnose, report, and automatically improve de novo genome assemblies as
well as call variants.\"
## General Linux

To run this software interactively in a Linux environment use the commands:

    module load pilon

    pilon [options]

Because this software uses an alias to create the pilon command, to use this software in a Slurm 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](https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage)