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Max qscore sum at differences (-d). If an overlap contains lots of differences at bases of high quality, then the overlap is removed. The difference score is calculated as follows. If the overlap contains a difference at bases of quality values q1 and q2, then the score at the difference is max(0, min(q1, q2) - b), where b is Quality cutoff for differences. The difference score of an overlap is the sum of scores at each difference.

If the similarity score of an overlap is less than the overlap similarity score cutoff (-s), then the overlap is removed. The similarity score of an overlapping alignment is defined using base quality values as follows. A match at bases of quality values q1 and q2 is given a score of m * min(q1,q2), where m is Match score factor. A mismatch at bases of quality values q1 and q2 is given a score of n * min(q1,q2), where n is Mismatch score factor. A base of quality value q1 in a gap is given a score of -g * min(q1,q2), where q2 is the quality value of the base in the other sequence right before the gap and g is Gap penalty factor. The score of a gap is the sum of scores of each base in the gap minus a gap open penalty. The similarity score of an overlapping alignment is the sum of scores of each match, each mismatch, and each gap. 

This parameter allows one to trade off the efficiency of the program for its accuracy (parameter -t of CAP3). For a read f, CAP3 computes overlaps between read f and other reads by considering short word matches between read f and other reads. A word match is examined to see if it can be extended into a long overlap. If read f has overlaps with many other reads, then read f has many short word matches with many other reads. This parameter gives an upper limit, for any word, on the number of word matches between read f and other reads that are considered by CAP3. Using a large value for this parameter allows CAP3 to consider more word matches between read f and other reads, which can find more overlaps for read f, but slows down the program. Using a small value for this parameter has the opposite effect.

The maximum length of gaps allowed in any overlap (-f). I.e. overlaps with longer gaps are rejected. Note that a small value for this parameter may cause the program to remove true overlaps and to produce incorrect results. The parameter may be used to split reads from alternative splicing forms into separate contigs.

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