I want to ask your opinion on the following subject:
Currently, we are producing synthesized DNA with the use of Multiply-Primed Rolling Circle Amplification. This allows for the production of a lot of DNA. Within that DNA there is a region which can be used for gene therapy. To be sure that our DNA polymerase didn't introduce too many errors (the error rate is 1 for every 1.000.000 bases), a QC has to be made. We want to use MinION for this. Now we are thinking of 2D sequencing (using our own caps to achieve this). Next to that is the data analysis, which is a bit more complicated due to the fact that most SNP variant callers are used in WG analysis. What I would like to ask is, what do you guys think of the 2D sequencing step to improve accuracy? And what are your suggestions on the data analysis? We are currently thinking of P.E.P.P.E.R. (https://github.com/kishwarshafin/pepper). But this seems like a bit overkill maybe.
I am looking forward to what you guys think.