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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 -O /export/apps/pilon/1.23/pilon-1.23.jar
pilon-software.txt · Last modified: 2019/02/15 09:14 by aorth