Yufan Fan from Johns Hopkins University presented at the Nanopore Community Meeting in December 2017. I had not watched this session, and the title captured my attention: Bacterial DNA modifications with Nanopore sequencing. This session was short and full of information. Fan spoke about how bacteria can unleash endonucleases to cut foreign DNA. Their own DNA is often methylated for protection. Bacteria can perform a variety of methylations! Courtesy of NEB, Fan examined the electrical current produced when sequencing DNA with different methylation patterns. Using Nanopolish methyltrain, Fan produced distributions for methylated bases in selected kmers. Fan analyzed different methylation patterns based on the current distributions produced when sequencing the methylated molecules from NEB. Fan trained the methylation model using a variety of enzyme motifs. I wonder if these models have been updated and are available for use!
