Paired-End vs. Single-Read Sequencing

Paired-end sequencing

• Simple paired-end libraries: Simple workflow allows generation of unique ranges of insert sizes
• Efficient sample use: Requires the same amount of DNA as single-read genomic DNA or cDNA sequencing
• Broad range of applications: Does not require methylation of DNA or restriction digestion; can be used for bisulfite sequencing
• Simple data analysis: Enables high-quality sequence assemblies with short-insert libraries. 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.

Single-read sequencing

• Cost-effective uses: This solution delivers large volumes of high-quality data, rapidly and economically
• Specific applications: Single-read sequencing can be a good choice for certain methods such as small RNA-Seq or chromatin immunoprecipitation sequencing (ChIP-Seq)

Paired-end DNA 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

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.