Merging overlapping reads. (A) Reads are slid along each other until the number of matches exceeds the significance threshold. In the example shown, the optimal overlap is 74 nucleotides (nt). (B) The quality of reads declines dramatically toward their 3’ ends, where overlap occurs if the fragment length is less than twice the read length, allowing the actual quality to be much higher than the nominal values. The example shown is the average of pairs that overlap by exactly 50 nt.