Extract Iupacsuffix

ExtractIUPACSuffix #

[[step]]
    action = "ExtractIUPACSuffix"
    label = "mytag"
    query = "AGTCA"  # the adapter to trim. Straigth bases only, no IUPAC.
    segment = "read1"   # Any of your input segments (default: read1)
    min_length = 3     # uint, the minimum length of match between the end of the read and
                       # the start of the adapter
    max_mismatches = 1 # How many mismatches to accept

Find a potentially truncated IUPAC sequence at the end of a read.

Simple comparison with a max mismatch hamming distance, requiring only the first min length bases of the query to match at the end of the read.

Trim with TrimAtTag if you want to remove the found suffix.