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

• Version: 1.23
• Added: November, 2018
• Updated: February, 2019
• Link: https://github.com/broadinstitute/pilon/wiki

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

$ java -Xmx8G -jar /export/apps/pilon/1.23/pilon-1.23.jar

The documentation recommends using a minimum of 8GB of memory, or 16GB if possible. As a rule of thumb, try to allocate 1GB of memory per megabase of input genome to be processed.

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/pilon/1.23
$ sudo wget https://github.com/broadinstitute/pilon/releases/download/v1.23/pilon-1.23.jar -O /export/apps/pilon/1.23/pilon-1.23.jar