Hi,

I am going to get some data from plasmid sequencing to identify SNPs on the plasmids. What it is done on the lab is the following:

 - The plasmids are purified by size
 - We amplify the plasmids using the phi29 polimerase. The polimerase will go trough the plasmid multiple times. Hence we get the same sequence concatenated multiple times. **My question is related to this step**
 - 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 try 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!
Thanks to this [answer][1] in bioinformatics stackexchange, there is a tool doing exactly what you want. The tool is called [C3P0a][2]


  [1]: https://bioinformatics.stackexchange.com/questions/5397/error-correction-within-the-long-read/5406#5406
  [2]: https://github.com/rvolden/C3POa