Good Ride

v2.0.0 — 2026-01-24

🎉 Major Release: Chao's Estimator

✨ New Features

• Added gt-estimator command — New primary command for sequencing saturation estimation using Chao's estimator. For more detailed info check the README.

  • Implements a CpG sequencing saturation estimator developed by Chao Deng et al. (2018)
  • Built on the preseqR framework
  • Extrapolates CpG predictions to higher sequencing depths
  • Distinguishes between interpolated (t ≤ 1) and extrapolated (t > 1) predictions
  • Supports confidence interval computation via bootstrap resampling (--compute_ci flag)

• New output format — methurator_summary.yml with Chao estimator results

  • Includes extrapolation factor (t) values from 0 to t_max
  • Boolean indicating interpolated vs extrapolated data
  • Confidence intervals (if enabled)
  • Model parameters and command options

📋 Notes

• The downsample command remains available for backward compatibility
• Existing methurator_summary.yml format unchanged for downsample workflow