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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


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