PILON

Description

pilon website  

Pilon is a software tool which can be used to:

• Automatically improve draft assemblies
• Find variation among strains, including large event detection

Environment Modules

Run module spider pilon to find out what environment modules are available for this application.

System Variables

• HPC_PILON_DIR - installation directory
• HPC_PILON_BIN - executable directory
• HPC_PILON_DOC - documentation directory

Additional Information

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...]

Citation

If you publish research that uses pilon you have to cite it as follows:

Bruce J. Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K. Young, Ashlee M. Earl (2014) Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 9(11): e112963. doi:10.1371/journal.pone.0112963