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