Mefystos

Mefystos analyzes aligned BAM files containing modified-base calls. Two commands share one YAML configuration: quality produces an interactive quality report; methyl produces methylation pileups, count tables, optional BigWig tracks and differentially methylated regions (DMR).

Start with the reproducible tutorial, then adapt the configuration reference to your data. This documentation tracks the code in the same Git revision; see migration notes when updating an existing analysis.

User guide

• Installation
  • Python package
  • External tools
• Reproducible tutorial
  • Generate inputs
  • Inspect and run
  • Compare a control with all other conditions
  • Use real data
• Prepare input data
  • BAM list
  • Regions
• Configuration reference
  • global
  • quality
  • coverage
  • summary
  • sample_probs
  • pileup
  • bigwig
  • dmr
  • Additional arguments and compatibility
• Quality workflow
  • Coverage and report size
• Methylation workflow
  • Pileup and reuse
  • Count tables
  • BigWig
  • Preview and logs
• Differential methylation
  • Choose comparisons
  • Multi example
  • Sites, regions and segments
• Output files and interpretation
  • Quality TSVs
  • Coverage columns
  • Raw count BED
  • Tracks and DMR
• Troubleshooting
• Changes and configuration migration
  • Unreleased
  • July 28, 2026 — b81eda4
  • July 27, 2026 — bc34d79
  • July 23, 2026 — 92c4da0 / 9c53858
• Maintain and publish the documentation
  • Local build
  • Validation
  • Read the Docs activation