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


===== Information =====

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

===== Usage =====

Pilon is distributed as a Java JAR file. You need to run it like this:
<code>$ java -Xmx8G -jar /export/apps/pilon/1.23/pilon-1.23.jar</code>

The [[https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage|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.

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>