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README.md

pilon container

Main tool : pilon

Additional tools (required):

  • java (specifically openjdk-11-jre)

Example Usage

Note: both BAM files must be indexed with samtools index prior to usage

java -jar -Xmx16G /pilon/pilon.jar \
  --genome fasta --frags paired_bam \
  --unpaired unpaired_bam \
  --output outdir \
  --changes

WARNING : pilon is included as a jarfile at /pilon/pilon-${PILONVER}.jar and copied to /pilon/pilon.jar

Also, memory issues are common with pilon. From their documentation:

Generally, bacterial genomes with ~200x of Illumina coverage will require at least 8GB, though 16GB is recommended. Larger genomes will require more memory to process; exactly how much is very data-dependent, but as a rule of thumb, try to allocate 1GB per megabase of input genome to be processed.