Originally posted by Mchicken
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Consider a typical monotonic dropping quality - first you might want to decide where the window drops below the threshold, then remove the later, weaker bases within the window, but keep the earlier, stronger ones. To achieve this, you need to first find the window, then decide how much to keep.
Once the window is found (very likely in the position you expect), the individual bases are checked against the required quality from the end of the window backwards. In your example, the last base is somewhat stronger than the threshold, so removal stops there.
An obvious alternative would be to start at the beginning of the window, and cut at the first weak base. When i compared the two approaches, the 'from the back' approach seemed to work better, so trimmomatic uses this.
Hope this helps,
Tony.
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