Fig. 1: Analysis pipeline for 5mC detection at CpG sites from nanopore sequencing. | Nature Communications

Fig. 1: Analysis pipeline for 5mC detection at CpG sites from nanopore sequencing.

From: Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing

Fig. 1

The diagram describes the approach used to test the tools Nanopolish, Tombo, DeepSignal, Megalodon, Guppy, and DeepMod. Snakemake pipelines and command lines used are available at https://github.com/comprna/METEORE11. A Snakemake pipeline was not developed for Megalodon and DeepMod as they can be run with a single command. Excluding DeepMod, all tools produce predictions per individual read and per CG site. In addition, all tools predict the methylation frequency at each genome site from fast5 input files. Methods that currently only accept single-read fast5 format are indicated.

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