text: user706: I am going to get some data from plasmid sequencing to identify SNPs on the plasmids. What is done in the lab is the following:
  
  The plasmids are purified by size.
  We amplify the plasmids using the phi29 polymerase. The polymerase will go through the plasmid multiple times. Hence we get the same sequence concatenated multiple times. My question is related to this step: 
  Finally, We sequence it using Oxford Nanopore.
  
  My question is:
  On step two, I wrote that "we get the same sequence concatenated multiple times". For me, this a potential source of information to correct the base calls prior to aligning them to the reference. Since you have the same sequence multiple times (concatemers). 
  What I would like to know is if there is a tool that uses the information of the concatemers to improve the base calls. I have tried to find some methods but found none. I know that PacBio has a similar flavour using the "circular consensus calling", but I have not found any methodological explanation.
  thanks!
  
  user2085: Yes, there is a tool to do this called R2C2 by the Vollmers lab at UC Santa Cruz.
  https://www.biorxiv.org/content/early/2018/06/04/338020
  
original_text: 706: <p>I am going to get some data from plasmid sequencing to identify SNPs on the plasmids. What is done in the lab is the following:</p>
  
  <ul>
  <li><p>The plasmids are purified by size.</p></li>
  <li><p>We amplify the plasmids using the phi29 polymerase. The polymerase will go through the plasmid multiple times. Hence we get the same sequence concatenated multiple times. <strong>My question is related to this step:</strong> </p></li>
  <li><p>Finally, We sequence it using Oxford Nanopore.</p></li>
  </ul>
  
  <p>My question is:</p>
  
  <p>On step two, I wrote that "we get the same sequence concatenated multiple times". For me, this a potential source of information to correct the base calls prior to aligning them to the reference. Since you have the same sequence multiple times (concatemers). </p>
  
  <p>What I would like to know is if there is a tool that uses the information of the concatemers to improve the base calls. I have tried to find some methods but found none. I know that PacBio has a similar flavour using the "circular consensus calling", but I have not found any methodological explanation.</p>
  
  <p>thanks!</p>
   2085: <p>Yes, there is a tool to do this called R2C2 by the Vollmers lab at UC Santa Cruz.</p>
  
  <p><a href="https://www.biorxiv.org/content/early/2018/06/04/338020" rel="nofollow noreferrer">https://www.biorxiv.org/content/early/2018/06/04/338020</a></p>
  