Single-read sequencing involves sequencing DNA from only one end, and is the simplest way to utilize Illumina sequencing. Unlike single-read seqeuncing, 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 more difficult 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.
Paired-end RNA sequencing (RNA-Seq) enables discovery applications such as detecting gene fusions in cancer and characterizing novel splice isoforms.2
For paired-end RNA-Seq, Illumina offers kits with an alternate fragmentation protocol, followed by standard Illumina paired-end cluster generation and sequencing.
A simple, scalable, cost-effective, rapid single-day solution for analyzing the coding transcriptome.
Rapid library preparation from a broad range of sample types for studying the coding and non-coding transcriptome with exceptional study flexibility.
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Learn about the advantages of short-paried reads over long single reads across the same sequencing length in this paper.