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:

Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K., & Earl, A. M. (2014). Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE, 9(11), e112963. https://doi.org/10.1371/journal.pone.0112963

Categories¶

biology, ngs, phylogenetics