Leading qualitytrim option.
Maximum mismatch density. See user options below for more information.
$is appended, the adapter is only found if it is at the end of the read. Maximum 250bp.
^character is prepended, the adapter is only found if it is at the beginning of the read. Maximum 250bp.
Front 5' adapterare allowed. If the first base of the read is part of the match, the behavior is as with
Front 5', otherwise as with
3' adapter. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Maximum 250bp.
required quality. Specifies the number of bases to average across. (default: 4)
Minimum overlap: The minimum required overlap length between two reads to provide a confident overlap. (default: 10)
Maximum overlap: Maximum overlap length expected in approximately 90% of read pairs. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, but the
mismatch density (explained below) is only calculated over the first
max_overlap bases in the overlapped region rather than the entire overlap. (default: 315)
Minimum outie overlap: The minimum required overlap length between two reads to provide a confident overlap in an "outie" scenario. (default: 35)
Maximum mismatch density: Maximum allowed ratio between the number of mismatched base pairs and the overlap length. (default: 0.25)