Systematic benchmarking of detection tools for CpG methylation from nanopore sequencing

Traditional Methylation profiling requires specific chemical treatment and downstream preparation such as immunoprecipitation, enzyme digestion or bisulfite conversion. Nanopore sequencing provides the opportunity to assess native DNA enabling the direct detection of bases, modified bases, and methylation.

However, there has been no systematic benchmarking to assess the tools used for calling such modifications. In this talk Zaka determines the strength and limitations of the following tools: Nanopolish, Tombo, DeepSignal, Megalodon and Guppy in the detection of 5-methylcytosine (5mC) in the context of CpG using a single MinION flow cell in comparison with standard bisulfite method.

Zaka concluded nanopore sequencing showed good correlation to bisulfite data with DeepSignal displaying the best performance and nanopore can detect methylation accurately even at low coverage."