Select Sequence Range From [x] Bases to [y] Bases

Certain base pair ranges in the sequence reads can be masked. Select this option to ensure that only this specified range of base pairs is loaded for alignment and compared to the reference.

Hide Unmatched Ends

Hides the ends of reads that do not match to the reference, which can reduce the false positive detection rate. NextGENe hides the unmatched ends by checking for two mismatches in the last eight base pairs, and then trimming to the mismatched base. It repeats this process until eight base pairs are found without two mismatched ends.