Table 1 Comparison of CpG methylation frequencies from whole-genome bisulfite sequencing (WGBS) and from Cas9-targeted nanopore data.

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

 

N

r

r2

ρ

RMSE

Nanopolish

1704

0.8652

0.7485

0.8326

0.2248

DeepSignal

1731

0.9177

0.8423

0.8765

0.1708

Megalodon

1723

0.9117

0.8312

0.8801

0.1772

Tombo

1661

0.7765

0.6030

0.7537

0.2996

Guppy

1738

0.8513

0.7246

0.8316

0.2334

DeepMod

1739

0.7401

0.5477

0.7264

0.2874

METEORE (RF)

1723

0.9174

0.8416

0.8862

0.1829

METEORE (REG)

1723

0.9262

0.8579

0.8885

0.1607

  1. For each method, we give the number of sites (N), the Pearson’s correlation (r), coefficient of determination (r2), the Spearman’s rank correlation (ρ), and the root mean square error (RMSE) for the comparison of the percentage methylation predicted from nanopore with the percentage methylation calculated from WGBS Illumina data. We show the results for the six tested tools and METEORE combining Megalodon and DeepSignal using a random forest (RF) (parameters: max_depth = 3 and n_estimator = 10) or a regression (REG) model.
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