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:
  • Contigs: Number of contigs.
  • Assembled BP: Number of assembled base pairs.
plotData:
  • size_dist: Distribution of contig size.
  • sparkline: Number of assembled base pairs.
  • genomeSliding:
    • gcData: Genome sliding window of GC content.
    • covData: Genome sliding window of read coverage depth.
    • window: Size of sliding window
    • xbars: Position of contigs along the genome sliding window.
    • assemblyFile: Name of the input assembly file.
warnings:
  • When the number of contigs exceeds a given threshold.
fail:
  • When the genome size is below 80% or above 150% of the expected genome size.