🧬 methurator

methurator is a Python package to estimate CpG sequencing saturation for DNA methylation sequencing data. It supports two complementary approaches:

  1. Chao's estimator (recommended)
  2. Empirical downsampling

Key features

  • Extrapolate CpG discovery beyond observed sequencing depth
  • Compute theoretical asymptotes
  • Optional bootstrap confidence intervals
  • Interactive HTML plots
  • BioConda and BioContainer support

Installation

Pip

Dependencies

If you install methurator via pip, be sure to install its dependencies SAMtools and MethylDackel.

pip install methurator

BioConda

conda create -n methurator_env conda::methurator
conda activate methurator_env

BioContainer

docker pull quay.io/biocontainers/methurator:2.1.1--pyhdfd78af_0
docker run quay.io/biocontainers/methurator:2.1.1--pyhdfd78af_0 methurator -h