Usage

Basic usage:

$ module load pilon/1.24

$ pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam [...other options...]

For additional usage information, use the following:

$ pilon --help

If you need additional java heap memory, you can use the command:

$ java -Xmx60G -jar /apps/pilon/1.24/share/pilon-1.24-0/pilon.jar --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam [...other options...]