<p>They are all very different in separate regards, but they all refer to different wet-lab and sequencing protocols/technologies.</p>
<p>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:</p>
<pre><code>------&gt; PE1
-------------------------------- Fragment
                         &lt;------ PE2
       ^^^^^^^^^^^^^^^^^^        Insert
</code></pre>
<p>In contrast mate pairs arise from a fragment that is circularized before sequencing. Now imagine the fragment is circularized:</p>
<pre><code>                     -----&gt; MP1
....--------------------------------.......
          MP2 &lt;-----
                    ^Circularized (joined) here
</code></pre>
<p>Long reads typically refer to PacBio or Oxford nanopore data, with very long reads lengths (up to several hundred kb).</p>

CC BY-SA 4.0
2020-10-17T16:57:41.483Z
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
CC BY-SA 4.0
2020-10-17T13:14:41.990Z
2020-10-17T13:14:41.990Z
Bastian Schiffthaler
<p>I writing here because I have some questions for you.</p>
<p>I wondered what the essential differences were between <code>paired-end</code>, <code>mate-pair</code> and <code>long read</code>?</p>
<p>for me <code>mate-pair</code> and classic <code>paired-end</code> are both <code>paired-end reads</code>, with the difference that :</p>
<ol>
<li>For classical <code>paired-end</code>: the insert size on classic paired-end is
smaller (about 500bp)</li>
<li>while the insert size of <code>mate-pair</code> is much longer (several Kb)
which allows to join the contiguous between them especially is it?</li>
</ol>
<p>In revenge for the <code>long-reads</code>, 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?</p>

<assembly><read-mapping><long-reads>
Difference between paired-end, mate-pair and long read
# Difference between paired-end, mate-pair and long read

(Asked by: username_0 on 2020-10-17)

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?

**Tags:** assembly, read-mapping, long-reads

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## 1 answers

### Answer by username_1 on 2020-10-17. Score: 4 | Accepted answer

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).

> **Comments:**
> **username_0**: 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...  

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