Extract Poly Tail

ExtractPolyTail #

[[step]]
    action = "ExtractPolyTail"
    label = "tag-label"
    segment = "read1" # Any of your input segments (default: read1)
    min_length = 5 # positive integer, the minimum number of repeats of the base
    base = "A" # one of AGTCN., the 'base' to trim (or . for any repeated base)
    max_mismatch_rate = 0.1 # float 0.0..=1.0, how many mismatches are allowed in the repeat
    max_consecutive_mismatches = 3 # how many consecutive mismatches are allowed

[[step]]
    action = "TrimAtTag"
    label ="tag-label"
    direction = "End"
    keep_tag = false

Identify either a specific base repetition, or any base repetition at the end of the read.

Trimming on this may produce empty reads, See the warning about empty reads.

Together, this is similar to fastp’s trim_poly_g/trim_poly_x but with a different implementation.