Welcome to pydamage’s documentation!

Homepage: github.com/maxibor/pydamage

Contents:

• PyDamage
  • Installation
  • Quick start
  • CLI help
  • Documentation
  • Cite
• API
  • pydamage_analyze()
• CLI
  • pydamage
• Output
  • pydamage_results.csv
  • pydamage_filtered_results.csv
  • pydamage_rescaled.bam
  • Plots
  • Example
• Troubleshooting
  • My alignment files don’t have a MD tag
  • I have filtered my BAM file to only retain a few references but pyDamage is still iterating across all references
• Rescaling
  • Rescaling base quality scores using aDNA damage profile

Indices and tables

• Index

• Module Index

• Search Page