process_skesa

Purpose

This components processes the assembly resulting from the Skesa software and, optionally, filters contigs based on user-provide parameters.

Input/Output type

  • Input type: Fasta
  • Output type: Fasta

Note

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

Parameters

  • skesaMinKmerCoverage: Minimum contigs K-mer coverage. After assembly only keep contigs with reported k-mer coverage equal or above this value.
  • skesaMinContigLen: Filter contigs for length greater or equal than this value.
  • skesaMaxContigs: Maximum number of contigs per 1.5 Mb of expected genome size.

Published results

None.

Published reports

  • reports/assembly/skesa_filter: The filter status for each contig and each sample. If any contig does not pass the filters, it reports which filter type it failed and the corresponding value.

Default directives

  • container: ummidock/skesa
  • version: 0.2.0-3

Advanced

Template

flowcraft.templates.process_assembly

Reports JSON

tableRow:
  • Contigs (<assembler>): Number of contigs.
  • Assembled BP (<assembler>): Number of assembled base pairs.
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.