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This analysis generates in-silico mixtures at different ratios and reconstructs co-occurring ecDNA elements using Decoil.

3.1 Pair-wise mixtures of ecDNA containing samples at different ratios

  • Generate in-silico mixtures
  • Reconstruct ecDNA elements in mixtures
  • Aggregate all found SVs for downstream analysis
cd ../ecDNA_mixtures

# create environment
bash install.sh

# Generate mixtures, reconstruct ecDNA in mixtures and aggregate results
bash runs.sh

3.2 Compute amplicon recovery for the mixtures

Install:

  • jupyter-lab
  • python>=3.8
    • pysam
    • numpy
    • pandas
    • rpy2
  • R>4.1.1
    • ggplot2

See AmpliconRecovery.ipynb notebook. Output breakpoints_recovery_merged.png (https://doi.org/10.5281/zenodo.10785693).