CalcNCount #

[[step]]
    action = "CalcNCount"
    segment = "read1" # Any of your input segments, or 'All'
    out_label="ncount"

Count how many N are present in the read.

This step is a convenient wrapper for CalcBaseContent with bases_to_count = "N" and relative = false.

Corresponding options in other software #

• fastp: –n_base_limit (if combined with FilterByNumericTag)