What is the difference between paired-end and mate pair?

What is the difference between paired-end and mate pair?

Overview. To simplify, you can differ between two kinds of reads for paired-end sequencing: short‑insert paired‑end reads (SIPERs) and long-insert paired-end reads (LIPERs). The latter one is also called mate pair. The difference between the two variants is first – surprise – the length of the insert.

Is Illumina sequencing paired-end?

All Illumina next-generation sequencing (NGS) systems are capable of paired-end sequencing.

What is paired-end sequencing?

The library preparation for “paired-end” sequencing, according to the lllumina technology, consists in fragmenting the genomic DNA mechanically (Covaris, Bioruptor) or enzymatically (tagmentase) to sizes below 1 kb.

How are paired-end reads paired?

The term ‘paired ends’ refers to the two ends of the same DNA molecule. So you can sequence one end, then turn it around and sequence the other end. The two sequences you get are ‘paired end reads’.

Does Illumina sequence both strands?

Illumina gets sequence data from both strands of input sequence which means it outputs data from both ends of the input and is normally reported two files R1 and R2, often refereed to as mates files (R1=first mates, R2=second mates).

What is the difference between single end and paired-end sequencing?

Single-end vs. In single-end reading, the sequencer reads a fragment from only one end to the other, generating the sequence of base pairs. In paired-end reading it starts at one read, finishes this direction at the specified read length, and then starts another round of reading from the opposite end of the fragment.

What is single-end and paired-end?

What are mate pair reads?

Mate pair sequencing involves generating long-insert paired-end DNA libraries useful for a number of sequencing applications, including: De novo sequencing. Genome finishing. Structural variant detection.