Awesome

Scripts and analysis for the Giurgiu et al. Genome Research 2024. "Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil".

Software release:

• Decoil tool: decoil-pre-1.1.2-slim
• Decoil vizualization tools: decoil-viz-1.0.3
• Simulate ecDNA templates: ecDNA-sim-1.0.0
• Simulate reads using a circular .fasta with an improved pseudonumber generator (adapted PBSIM2): pbsim2-1.0.0beta.zip 
• Pipeline for simulating and processing ecDNA: ecDNA-simulate-validate-pipeline-1.0.1

Linked repositories:

• https://github.com/madagiurgiu25/decoil-pre
• https://github.com/madagiurgiu25/decoil-viz
• https://github.com/madagiurgiu25/ecDNA-sim
• https://github.com/madagiurgiu25/ecDNA-simulate-validate-pipeline
• https://github.com/madagiurgiu25/pbsim2

Zenodo

To access the data linked to this analysis go to https://zenodo.org/uploads/10785693. The raw have been submitted to the EGA repository (https://ega-archive.org/) under studies EGAS50000000348 and EGAS50000000349.

Code and analysis for the paper (overview):

• 1. Decoil development

  • Decoil
  • Decoil-viz
  • Linear models comparison to deconvolve ecDNA elements from simulated overlapping fragments data

• 2. Simulations and benchmarking

  • Simulate ecDNA sequence templates (.fasta)
  • Simulate and pre-process in-silico long-read ecDNA-containing samples (.fastq, .bam, .bw, .vcf)
  • Alignment-free ecDNA reconstruction using Shasta from simulated data
  • Alignment-based ecDNA reconstruction using Decoil from simulated data
  • Alignment-based ecDNA reconstruction using CReSIL from simulated data
  • Performance evaluation on simulated data for Decoil, Shasta and CReSIL

• 3. Generate ecDNA mixtures and evaluate amplicon's breakpoints

  • Downsampling to 10,25,50,75,90% for the three celllines
  • Generate mixtures 100-10, 100-25, 100-50, 100-75, 100-90%
  • Process all mixtures, i.e. SV calling, Decoil reconstruction, aggregate results
  • Compute amplicion breakpoints recovery in the dilutions

• 4. ecDNA reconstruction for cellines and patient data

  • Preprocess nanopore sequencing data from cell lines and patient samples
  • Reconstruct ecDNA elements for cell lines using Decoil
  • Reconstruct ecDNA elements for patient samples using Decoil
  • Perform de-novo assembly for cell lines using Shasta
  • Compare Decoil and Shasta outputs against the against published ecDNA structures

• 5. Paper figures

<br/><br/>

1. Decoil development

Go to decoil.

2. Simulations and benchmarking

This part of the paper describes the ecDNA simulation and performance evaluation.

Go to simulations and benchmarking.

3. Evaluate amplicon's breakpoints recovery in ecDNA mixtures

Pair-wise mixtures of ecDNA containing samples at different ratios and reconstruction of co-occurring ecDNA elements using Decoil.

Go to mixtures.

4. ecDNA reconstruction for cellines and patient data

Apply Decoil on celllines and patient data. Go to reconstruction.

Additionally, the reconstruction and de-novo assembly for cell lines are compared against validated structures. Go to comparison.

5. Paper figures

Go to ../data/figures.

Citation

If you use this code please cite our publication:

Madalina Giurgiu, Nadine Wittstruck, Elias Rodriguez-Fos, Rocio Chamorro Gonzalez, Lotte Bruckner, Annabell Krienelke-Szymansky, Konstantin Helmsauer, Anne Hartebrodt, Philipp Euskirchen, Richard P. Koche, Kerstin Haase*, Knut Reinert*, Anton G. Henssen*.Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil. Genome Research 2024, DOI: https://doi.org/10.1101/gr.279123.124

@article{Giurgiu2024ReconstructingDecoil,
    title = {{Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil}},
    year = {2024},
    journal = {Genome Research},
    author = {Giurgiu, Madalina and Wittstruck, Nadine and Rodriguez-Fos, Elias and Chamorro Gonzalez, Rocio and Brueckner, Lotte and Krienelke-Szymansky, Annabell and Helmsauer, Konstantin and Hartebrodt, Anne and Euskirchen, Philipp and Koche, Richard P. and Haase, Kerstin and Reinert, Knut and Henssen, Anton G.},
    month = {8},
    pages = {gr.279123.124},
    doi = {10.1101/gr.279123.124},
    issn = {1088-9051}
}

License

The code is distributed under BSD-3-Clause license. See LICENSE for details.

Contact

For any questions do no hesitate to contact us.<br/> Author: Madalina Giurgiu (madalina.giurgiu@charite.de)