Scripts and analysis for the Giurgiu et al. Genome Research 2024. "Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil".
- 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
- 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
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.
-
- 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
Go to decoil.
This part of the paper describes the ecDNA simulation and performance evaluation.
Go to simulations and benchmarking.
Pair-wise mixtures of ecDNA containing samples at different ratios and reconstruction of co-occurring ecDNA elements using Decoil.
Go to mixtures.
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.
Go to ../data/figures.
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}
}
The code is distributed under BSD-3-Clause license. See LICENSE for details.
For any questions do no hesitate to contact us.
Author: Madalina Giurgiu ([email protected])