Pilon is a software tool which can be used to automatically improve draft assemblies find variation among strains, including large event detection.

• Version: 1.24
• Added: November, 2018
• Updated: May, 2025
• Link: https://github.com/broadinstitute/pilon

See which versions are available:

$ module avail pilon

Load one version into your environment and run it:

$ module load pilon/1.24
$ pilon

Note: the documentation recommends using a minimum of 8GB of memory. As a rule of thumb, try to allocate 1GB of memory per megabase of input genome to be processed. To override the default memory allocation you will need to run Pilon directly, for example::

$ java -Xmx16G -jar /export/apps/pilon/1.24/pilon-1.24.jar

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/pilon/1.24
$ sudo wget https://github.com/broadinstitute/pilon/releases/download/v1.24/pilon-1.24.jar -O /export/apps/pilon/1.24/pilon-1.24.jar
$ # edit /export/apps/pilon/1.24/pilon
$ cat /export/apps/pilon/1.24/pilon
#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)
# Default to 8G of heap
java -jar -Xmx8G $PREFIX/pilon-1.24.jar $*
$ sudo chmod +x /export/apps/pilon/1.24/pilon