2:30:15 => <seed mismatches>:<palindrome clipthreshold>:<simple clip threshold>
- seedMismatches: specifies the maximum mismatch count which will still allow a full match to be performed
- palindromeClipThreshold: specifies how accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment.
- simpleClipThreshold: specifies how accurate the match between any adapter etc. sequence must be against a read..