pilon

Summary

• Module Name: pilon

• Support Level: Primary Support

• Software Access Level: Open Access

• Home Page: 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