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DRAGEN-FastQC

Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data

https://www.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html

DRAGEN has a number of different pipelines and outputs, including base calling, DNA and RNA alignment, and many others. Starting with the release of DRAGEN v3.6, it also supports primary analysis of sequencing data, modelled after the QC metrics generated by the widely used FastQC tool.

This module parses the output from that hardware-accelerated QC tool, and uses it to generate similar plots to both FastQC and MultiQC's current FastQC module. These plots are presented in their own section and module, such that they can be run indepedently or in conjunction with other MultiQC DRAGEN modules as desired.

  • <output prefix>.fastqc_metrics.csv
    • Pre-calculated positional QV quantiles
    • Mean QVs by read position and base
    • A histogram of estimated read-level qualities
    • A histogram of read lengths
    • A smoothed histogram of sample GC content
    • Average read quality values for each GC content bin
    • Positional prevalence of ambiguous bases
    • Positional base content
    • Adapter/Kmer sequence start positions

Quality score box plots​

By default, the box plots showing the range of quality scores are only shown if there are maximum 2 samples in the report. You can change this threshold with the following MultiQC config (eg. to max 10 samples):

dragen_fastqc:
  quality_range_boxplots_max_samples: 10

If you prefer, you can force MultiQC to generate these box plots for all samples using the following configuration:

dragen_fastqc:
  force_quality_range_boxplots: true

File search patterns​

dragen_fastqc:
  fn: "*.fastqc_metrics.csv"