Paired-End vs. Single-Read Sequencing

Paired-end sequencing allows users to sequence both ends of a fragment and generate high-quality, alignable sequence data. Paired-end sequencing facilitates detection of genomic rearrangements and repetitive sequence elements, as well as gene fusions and novel transcripts.

In addition to producing twice the number of reads for the same time and effort in library preparation, sequences aligned as read pairs enable more accurate read alignment and the ability to detect insertion-deletion (indel) variants, which is not possible with single-read data.¹ All Illumina next-generation sequencing (NGS) systems are capable of paired-end sequencing.

Paired-end DNA sequencing reads provide high-quality alignment across DNA regions containing repetitive sequences, and produce long contigs for de novo sequencing by filling gaps in the consensus sequence. Paired-end DNA sequencing also detects common DNA rearrangements such as insertions, deletions, and inversions.

Single-read sequencing involves sequencing DNA from only one end, and is the simplest way to utilize Illumina sequencing. This solution delivers large volumes of high-quality data, rapidly and economically. Single-read sequencing can be a good choice for certain methods such as small RNA-Seq or chromatin immunoprecipitation sequencing (ChIP-Seq).