Pilon 2016

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Pilon is a software tool which can be used to:

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

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

  • Single base differences
  • Small indels
  • Larger indel or block substitution events
  • Gap filling
  • Identification of local misassemblies, including optional opening of new gaps

Pilon then outputs a FASTA file containing an improved representation of the genome from the read data and an optional VCF file detailing variation seen between the read data and the input genome.

To aid manual inspection and improvement by an analyst, Pilon can optionally produce tracks that can be displayed in genome viewers such as IGV and GenomeView, and it reports other events (such as possible large collapsed repeat regions) in its standard output. ¹

Installed version(s)

This version is installed and currently available on environment hpc-env/6.4:


Using Pilon

If you want to find out more about Pilon on the HPC cluster, you can use the command

module spider Pilon

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load hpc-env 6.4
module load Pilon

Always remember: this command is case sensitive!

After loading Pilon, you should see a short introduction on how to start and use Pilon:

To execute Pilon run: java -Xmx8G -jar $EBROOTPILON/pilon.jar
Adjust the memory value according to the size of your input files


Pilon has a wiki which can be found here.