Paired-end sequencing allows users to choose the length of the insert and sequence either end of the insert, generating high-quality, alignable sequence data. Paired-end sequencing can detect rearrangements, including insertions and deletions (indels) and inversions. As paired end reads are more likely to align to a reference, the quality of the entire data set improves.
A simple modification to the standard single-read DNA library preparation facilitates reading both the forward and reverse template strands of each cluster during one paired-end read. Both reads contain long range positional information, allowing for highly precise alignment of reads.