simulate-damage 0.1.3

Simulate ancient DNA deamination damage on paired-end FASTQ files

simulate_damage

simulate_damage is a command-line tool that simulates ancient DNA (aDNA) deamination damage in paired-end FASTQ files. It introduces realistic C→T and G→A transitions at read ends and internally, allowing researchers to test pipelines under damage conditions typical of ancient samples.

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Features

• Supports .fastq and .fastq.gz
• Handles paired-end reads automatically
• Allows custom damage rates for 5′ and internal C→T (R1) and G→A (R2)
• Keeps original read qualities and structure
• Fully scriptable or callable via CLI

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Installation

pip install simulate_damage

## Example usage

simulate_damage \
  --r1 sample_R1.fastq.gz \
  --r2 sample_R2.fastq.gz \
  --out_r1 damaged_R1.fastq.gz \
  --out_r2 damaged_R2.fastq.gz \
  --ct5 0.03 --ctint 0.4 --ga3 0.01 --gaint 0.7 --overhang 10