ExtractMeanQuality #

[[step]]
    action = "ExtractMeanQuality"
    segment = "read1" # Any of your input segments, or 'All'
    label = 'tag_quality'

Calculate the ‘average quality’ (for threshold filtering).

This is typically a bad idea, see https://www.drive5.com/usearch/manual/avgq.html for a discussion of the issues.

For example, 140 x Q35 + 10 x Q2 reads have an ‘average’ phred of 33, but 6.4 expected wrong bases A read with 150 x Q25 has a much wores ‘average’ phred of 25, but a much lower expected number of errors at 0.5!

Corresponding options in other software #

• Trimmomatic: AVGQUAL:
• fastp: –average_qual