Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-08T18:41:53.750Z
Answers.Text: That was definetively the tool I was looking for. Thank you very much!
Answers.UserDisplayName: Praderas
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-08T13:51:49.430Z
Answers.LastActivityDate: 2018-11-08T13:51:49.430Z
Answers.UserDisplayName: conchoecia
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-08T10:22:37.460Z
Comments.Text: Nice project! Do you know the length of the (linearized) plasmids? I haven't heard of any tool similar to this but I don't usually analyze long-reads sequencing data. Good luck with your project
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-08T11:26:57.873Z
Comments.Text: I don't, the project aim is to detect which plasmids a bacteria contains. Thanks for your answer
Comments.UserDisplayName: Praderas
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-08T11:48:58.293Z
Comments.Text: Then the project is more complicated, because if you don't know the length of the repetitions of the plasmid you'll need to search for a range of size of the repetitions, which can be longer/more difficult (depending on how you compare the different portions of the reads)
Comments.UserDisplayName: llrs
Tags: <nanopore><long-reads><minion><literature-search><minimap2>
Title: Error correction within the long read
ThreadText: # Error correction within the long read
  
  (Asked by: username_0 on 2018-11-08)
  
  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!
  
  **Tags:** nanopore, long-reads, minion, literature-search, minimap2
  
  > **Comments:**
  > **username_1**: Nice project! Do you know the length of the (linearized) plasmids? I haven't heard of any tool similar to this but I don't usually analyze long-reads sequencing data. Good luck with your project  
  > **username_0**: I don't, the project aim is to detect which plasmids a bacteria contains. Thanks for your answer  
  > **username_1**: Then the project is more complicated, because if you don't know the length of the repetitions of the plasmid you'll need to search for a range of size of the repetitions, which can be longer/more difficult (depending on how you compare the different portions of the reads)  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-11-08. Score: 2 | Accepted answer
  
  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>
  
  > **Comments:**
  > **username_0**: That was definetively the tool I was looking for. Thank you very much!  
  
  ---
  
  