PILON¶

Description¶

Pilon is a software tool that automatically improves draft assemblies and finds variation among strains, including large event detection.

Note: export _JAVA_OPTIONS="-Xmx?g" where ? equals to the available memory.

Environment Modules¶

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

Environment Variables¶

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

Additional Usage 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

Categories¶

biology, ngs, phylogenetics