<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>

CC BY-SA 4.0
2018-11-08T18:41:53.750Z
That was definetively the tool I was looking for. Thank you very much!
Praderas
CC BY-SA 4.0
2018-11-08T13:51:49.430Z
2018-11-08T13:51:49.430Z
conchoecia
<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>

CC BY-SA 4.0
2018-11-08T10:22:37.460Z
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
llrs
CC BY-SA 4.0
2018-11-08T11:26:57.873Z
I don't, the project aim is to detect which plasmids a bacteria contains. Thanks for your answer
Praderas
CC BY-SA 4.0
2018-11-08T11:48:58.293Z
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)
llrs
<nanopore><long-reads><minion><literature-search><minimap2>
Error correction within the long read
# 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)  

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## 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!  

---

