Specifically, it:
It then optionally trims off poor quality regions from the end, using a threshold percentage of unwanted characters in a window which is moved along the sequence from the ends. The unwanted characters which are used are X's and N's (in nucleic sequences), optionally *'s, and optionally IUPAC ambiguity codes.
The program stops trimming the ends when the percentage of unwanted characters in the moving window drops below the threshold percentage.
Thus if the window size is set to 1 and the percentage threshold is 100, no further poor quality regions will be removed. If the window size is set to 5 and the percentage threshold is 40 then the sequence AAGCTNNNNATT will be trimmed to AAGCT, while AAGCTNATT or AAGCTNNNNATTT will not be trimmed as less than 40% of the last 5 characters are N's.
After trimming these poor quality regions, it will again then trim off any dangling gap characters from the ends .
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