Pilon

Purpose

This components Performs a mapping procedure of FastQ files into a their assembly and performs filtering based on quality criteria of read coverage and genome size.

Note

Software page: https://github.com/broadinstitute/pilon

Input/Output type

  • Input type: Fasta and FastQ
  • Output type: Fasta

Note

The default input parameter for fasta data is --fasta.

Parameters

None.

Published results

  • results/assembly/pilon: Stores the polished fasta assemblies for each sample.

Published reports

  • reports/assembly/pilon: Table with several summary statistics about the assembly for each sample.

Default directives

  • pilon:
    • cpus: 4
    • memory: 7GB (dynamically increased on retry)
    • container: ummidock/pilon
    • version: 1.22.0-2
  • process_assembly_mapping:
    • cpus: 1
    • memory: 7GB (dynamically increased on retry)
    • container: ummidock/pilon
    • version: 1.22.0-2

Advanced

Reports JSON

tableRow:
Trimmed (%): Percentage of trimmed nucleotides
plotData:
sparkline: Number of nucleotides after trimming

badReads: Number of discarded reads