Illustrations of paired-end sequencing. (A) illustrates two strands of a double strands of DNA are both sequenced in the direction from 5' to 3' and ligated with paired-end adapters. In the situation that the double strands of DNA have a length longer than or equal to the machine specific sequencing length, no adapter corresponding sequences will be appended in the obtained paired-end sequenced reads. (B) illustrates the "read through" situation that the double strands of DNA have a length smaller than the machine specific sequencing length, so that parts of the adapter sequences are sequenced as well. (C) illustrates the error-prone strategy the existing adapter trimmers used for handling adapter-trimming operation.