Pilon is a software tool which can be used to:

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


  • Pilon web site
  • Citation: 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


Usage on Bridges


To see what versions of Pilon are available type

module avail pilon

To see what other modules are needed, what commands are available and how to get additional help type

module help  pilon

To use Pilon, include a command like this in your batch script or interactive session to load the Pilon module:

module load pilon


Be sure you also load any other modules needed, as listed by the module help pilon command.