Difference between revisions of "PILON"
Jump to navigation
Jump to search
| Line 38: | Line 38: | ||
Basic usage: | Basic usage: | ||
| + | $ module load pilon/1.24 | ||
$ pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam [...other options...] | $ pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam [...other options...] | ||
Revision as of 15:03, 1 August 2024
Description
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: