Answers.Body: <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>
  
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Answers.Text: 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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Body: <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>
  
Tags: <assembly><read-mapping><long-reads>
Title: Difference between paired-end, mate-pair and long read
ThreadText: # 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
  
  
  ---
  
  ## 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...  
  
  ---
  
  