# Difference between paired-end, mate-pair and long read

I writing here because I have some questions for you.

I wondered what the essential differences were between paired-end, mate-pair and long read?

for me mate-pair and classic paired-end are both paired-end reads, with the difference that :

1. For classical paired-end: the insert size on classic paired-end is smaller (about 500bp)
2. while the insert size of mate-pair is much longer (several Kb) which allows to join the contiguous between them especially is it?

In revenge for the long-reads, I imagine that they are simply reads that are synthesized with a large read size but that do not allow like the maite-pair to make junctions between contigs?

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chippycentra is a new contributor to this site. Take care in asking for clarification, commenting, and answering. Check out our Code of Conduct.

They are all very different in separate regards, but they all refer to different wet-lab and sequencing protocols/technologies.

First, PE (paired end) reads are typically short (50-300) reads, most often Illumina HiSeq, MiSeq or NovaSeq protocols. Both pairs originate from a single fragment which is sequenced from either end:

------> PE1
-------------------------------- Fragment
<------ PE2
^^^^^^^^^^^^^^^^^^        Insert


In contrast mate pairs arise from a fragment that is circularized before sequencing. Now imagine the fragment is circularized:

                     -----> MP1
....--------------------------------.......
MP2 <-----
^Circularized (joined) here


Long reads typically refer to PacBio or Oxford nanopore data, with very long reads lengths (up to several hundred kb).

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Bastian Schiffthaler is a new contributor to this site. Take care in asking for clarification, commenting, and answering. Check out our Code of Conduct.
• thank you very much for your time, as you can see ATpoint gave a link where I also asked a question in respond to a post, sorry for the duplication... – chippycentra Oct 17 at 16:57