pairedend

Paired-end sequencing is a sequencing approach in which both ends of DNA fragments are sequenced, producing read pairs that originate from the same fragment. Each pair provides two reads with a known approximate distance between them, called the insert size, which aids in aligning reads and reconstructing longer sequences than single-end reads.

In typical workflows, DNA is fragmented, adapters are added, and sequencing is performed from both ends. The resulting data consist of paired reads, commonly denoted as R1 and R2. On platforms such as Illumina, read lengths commonly range from 2x100 to 2x250 bases, with insert sizes ranging from a few hundred to about a thousand bases, depending on the library strategy.

Applications of paired-end sequencing include de novo genome assembly, where paired reads help span repeats and improve contiguity; read mapping and variant detection, where mate constraints enhance alignment accuracy and enable detection of insertions, deletions, and structural variants; transcriptomics (RNA-seq), where paired reads improve exon connectivity and transcript assembly; and metagenomics, where longer-range information aids in distinguishing closely related organisms.

Advantages of this approach include improved alignment across repetitive regions, better assembly quality, more reliable variant calling, and the ability to phase haplotypes over short distances. Limitations involve higher sequencing costs and data complexity, as well as the need for specialized computational handling of mate information and insert-size distributions. Paired-end sequencing contrasts with single-end sequencing and with mate-pair sequencing, the latter providing longer-range information through different library preparation.