Handling of N bases

One of the techniques that DRAGEN uses to optimize handling sequences can lead to the overwriting the base quality score assigned to N base calls.

When you use the --fastq-n-quality and --fastq-offset options, the base quality scores are overwritten with a fixed base quality. The default values for these options are 2 and 33 to match the Illumina minimum quality of 35 (ASCII character #).