assembly_mapping

Purpose

This component performs a mapping procedure of FastQ files using their assembly as reference. The procedure is carried out with bowtie2 and samtools and aims to filter the assembly based on quality criteria of read coverage and expected genome size.

Note

  • bowtie2 documentation can be found here.
  • samtools documentation can be found here.

Input/Output type

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

Note

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

Parameters

  • minAssemblyCoverage: In auto, the default minimum coverage for each assembled contig is 1/3 of the assembly mean coverage or 10x, if the mean coverage is below 10x.
  • AMaxContigs: A warning is issues if the number of contigs is over this threshold.
  • genomeSize: Genome size estimate for the samples. It is used to check the ratio of contig number per genome MB.

Published results

None.

Published reports

None.

Default directives

  • assembly_mapping:
    • cpus: 4
    • memory: 5GB (dynamically increased on retry)
    • container: ummidock/bowtie2_samtools
    • version: 1.0.0-2
  • process_assembly_mapping:
    • cpus: 1
    • memory: 5GB (dynamically increased on retry)
    • container: ummidock/bowtie2_samtools
    • version: 1.0.0-2

Advanced

Reports JSON

plotData:
  • sparkline: Total number of base pairs.
warnings:
  • When the number of contigs exceeds a provided threshold.
fail:
  • When the genome size is below 80% or above 150% of the expected genome size.