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

• Version: 1.2.2
• Added: November, 2018
• Link: https://github.com/broadinstitute/pilon/wiki

Pilon is distributed as a Java JAR file. You need to run it like this:

$ java -Xmx16G -jar /export/apps/pilon/1.2.2/pilon-1.22.jar

The documentation recommends using a minimum of 8GB of memory, or 16GB if possible.

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/pilon/1.2.2
$ sudo wget https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar -O /export/apps/pilon/1.2.2/pilon-1.22.jar