Simulate ecDNA sequence templates (in .bed format).
This simulator aims to cover a large spectrum of ecDNA structure complexity, defined by the seven topologies in the Giurgiu et al. 2024: (i) Simple circularization, (ii) Simple SV's, (iii) Mixed SV's, (iv) Multi-region, (v) Multi-chromosomal, (vi) Duplications, (vii) Foldbacks.
git clone https://github.com/madagiurgiu25/ecDNA-sim
cd ecdna-sim
python -m pip install -e .
import main as m
import simulate as s
# simulate a multi-fragment rearranged ecDNA, allowing inversion, deletions, foldbacks, originating from multiple-chromosomes
conf = {N:3,
NEIGHBOR: False,
SINGLE_CHR: False,
WEIGHT_CHR: [50,50],
P_DEL_LEFT: 60,
P_DEL_RIGHT: 60,
P_INVERT: 40,
P_DUP: 0,
P_FOLDBACK: 40,
}
m.simulate_simple_mix(s.CHRLEN, s.CHRRANGES)
Check more examples under examples/01_Simulation.ipynb.
N- number of fragments [1-10]NEIGHBOR- is the next simulate fragment neighboring the pervious fragment [True/False]SINGLE_CHR- simulate ecDNA originating from a single chromosome [True/False]WEIGHT_CHR- weight each chromosomal regionP_DEL_LEFT- allow small deletions on the left side of the fragment with probability p [0-100]P_DEL_RIGHT- allow small deletions on the right side of the fragment with probability p [0-100]P_INVERT- allow inversion of the fragment with probability p [0-100]P_DUP- allow tandem duplication of the fragment with probability p [0-100]P_FOLDBACK- allow foldback, i.e. next fragment will overlap with the current one [0-100]
#chr start stop direction target coverage structure fragment
chr2 25294254 25594454 - circ_0 500 circ_0 0
chr2 25367069 25444784 + circ_0 500 circ_0 1
chr2 25367069 25444784 + circ_0 500 circ_0 2
chr2 25367069 25444784 + circ_0 500 circ_0 3
chr12 67786508 68089408 + circ_0 500 circ_0 4
chr2 10198624 10497524 - circ_0 500 circ_0 5
chr2 10278364 10387589 - circ_0 500 circ_0 6
chr2 10310394 10346800 - circ_0 500 circ_0 7
chr2 10338739 10352420 - circ_0 500 circ_0 8
chr2 10338739 10352420 - circ_0 500 circ_0 9
If you use Decoil for your work please cite our paper:
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}
}
Paper repository: https://github.com/henssen-lab/decoil-paper
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])