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.