DRAGEN FastQC

DRAGEN's FastQC module is a tool for calculating common metrics used for quality control of high-throughput sequencing data. The tool is modeled after the metrics generated by Babraham Institute's FastQC tool.

The metrics are generated automatically on all DRAGEN map-align workflows with no additional run time and output in a CSV format file called <PREFIX>.fastqc_metrics.csv.

For users only interested in sample QC or would like to obtain FastQC results only, DRAGEN provides a mode to generate the fastqc_metrics.csv file directly.

By default DRAGEN FastQC and read-trimming are run as preprocessing steps to standard sequence alignment workflows. If DNA alignment is not needed or if QC results are needed more quickly, the mapping and BAM output portions of the workflow can be disabled. The workflow only outputs key metric files and runs ~70% faster. This option is available on the command-line by entering --fastqc-only=true after the DRAGEN command.