Quality Control Workflows



FastQC is run on every FASTQ file to ensure the basic quality control. An html report is generated and linked from the FASTQ file metadata page.

Source Files

The pipeline components are pre-installed in a publicly available Docker image (4dndcic/fastqc:v2) on Docker Hub. The source code for the Docker image and pipeline description in Common Workflow Language (CWL) can be found on GitHub.

  • Latest runs

Content-wise, v1 and v2 can be considered (nearly) identical except that the latter does not include Kmer content in the output QC report.

  • v2
    • FastQC 0.11.9
    • CWL : https://github.com/4dn-dcic/docker-fastqc/tree/v2/cwl
    • Docker : https://github.com/4dn-dcic/docker-fastqc/tree/v2
  • v1
    • FastQC 0.11.5
    • CWL : https://github.com/4dn-dcic/docker-fastqc/tree/v1/cwl
    • Docker : https://github.com/4dn-dcic/docker-fastqc/tree/v1
  • sbg
    • A small portion of earlier data were run with FastQC version 0.11.4 using on Seven Bridges Genomics (SBG) using the Docker image / CWL on SBG.