downsample_fastq

Purpose

downsample_fastq uses seqtk to subsample fastq read data to a target coverage depth if the estimated coverage is higher than the provided target depth. When no subsample is required, it outputs the original FastQ files.

Note

Software page: https://github.com/lh3/seqtk

Input/Output type

  • Input type: fastq
  • Output type: fastq

Parameters

  • genomeSize: Genome size estimate for the samples. It is used to estimate the coverage.
  • depth: The target depth to which the reads should be subsampled.
  • seed: The seed number for seqtk. By default it is 100.

Published results

  • results/sample_fastq: Stores the subsampled FastQ files

Published reports

None.

Default directives

  • cpus: 1
  • memory: 4GB
  • container: flowcraft/seqtk
  • version: 1.3.0-3

Advanced

Reports JSON

tableRow:
  • Coverage: Estimated coverage.