Pilon

Software Description:

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.

Software Home Page: Pilon

Software Documentation:

To run this software in a Linux environment on LCC,
run the command(s):

#To load module
module load ccs/conda/pilon-1.23

#To unload module
conda deactivate