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.
Since paired-end reads are more likely to align to a reference, the quality of the entire data set improves. All Illumina NGS (next-generation sequencing) systems are capable of paired-end sequencing.
A simple modification to the standard single-read library preparation process 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.
Paired-end DNA sequencing reads provide superior alignment across DNA regions containing repetitive sequences, and produce longer contigs for de novo sequencing by filling gaps in the consensus sequence. Paired-end DNA sequencing also detects rearrangements such as insertions, deletions, and inversions.
Paired-end RNA sequencing (RNA-Seq) enables discovery applications such as detecting gene fusions in cancer and characterizing novel splice isoforms.
For paired-end RNA-Seq, use the TruSeq RNA Sample Prep Kits with an alternate fragmentation method, followed by standard Illumina paired-end cluster generation and sequencing.
For mRNA-Seq sample prep, use:
For stranded total RNA sample prep, use: