Hi, I'm planning to do sequencing using Nanopore.

The main idea is to substitute Sanger Sequencing that usually used to sequence PCR amplicon from BCD (Bisulfite Converted DNA) using nanopore device.

The experience that i have regarding nanopore data analysis is only alignments and variant calling.

the example is like this

on the bam file there would be many reads aligned to the reference

reference AATGCGTTTTT

read 1 AATGCGTTTTT

read 2 AATGTGTTTTT

read 3 AATGTGTTTTT

read 4 AATGCGTTTTT

read 5 AATGCGTTTTT

the %met would be 20%

I know this type of analysis could be easily done using tools like IGV or JBrowse to view the number of C/T reads in a specific position of the reference

but the problem is there is 40 samples, each sample will have 111 amplicon, and each amplicon contain around 35 CpG sites. so in total there would be more than 150k CpG site. Is there any efficient way to do this?