Visualize ecDNA reconstruction threads and summarize all the results generated by decoil.
To run `decoil-viz` you need to have installed [docker](https://docs.docker.com/engine/install/), and have docker engine running, or, [singularity](https://anaconda.org/conda-forge/singularity).
This image contains all the dependencies needed to run the software. No additional installation needed.
git clone https://github.com/madagiurgiu25/decoil-viz.git
cd decoil-viz
To download the docker image:
# for docker
./install.sh --docker
To download the singularity image:
# for singularity
./install.sh --singularity
With docker:
decoil-viz --docker --coverage <coverage_file> --summary <summary_file> --reference <reference_file> --gtf <gtf_file> --bed <bed_file> --links <links_file> --outdir <output_directory> --name <output_name>
With singularity:
decoil-viz --singularity --coverage <coverage_file> --summary <summary_file> --reference <reference_file> --gtf <gtf_file> --bed <bed_file> --links <links_file> --outdir <output_directory> --name <output_name>
To run a test example go to Example.
If you install decoil-viz from source, the prequisites are R>=4.1.1, python>=3.7 and git.
git clone https://github.com/madagiurgiu25/decoil-viz.git
cd decoil-viz
# install R dependencies
Rscript requirements.R
# install decoil-viz
python -m pip install .
# test installation
decoil-viz --help
Commandline usage:
Usage: decoil-viz [--docker|--singularity|--version|--help] --coverage <coverage_file> --summary <summary_file> --reference <reference_file> --gtf <gtf_file> --bed <bed_file> --links <links_file> --outdir <output_directory> --name <output_name>
Options:
-h,--help Display this help message
--version Display version
--docker Flag: run decoil-viz using docker (set by default if --singularity not active)
--singularity Flag: run decoil-viz using singularity
-o,--outdir <output_directory> Output directory (absolute path)
--name Sample name
--coverage <coverage_file> Coverage file in .bw format (absolute path)
--bed <bed_file> Reconstruction regions file in .bed like format (absolute path)
--links <links_file> Reconstruction links file in .txt format (absolute path)
--summary <summary_file> Reconstructions summary (absolute path)
-r,--reference <reference_file> Reference genome in .fasta format (absolute path)
-g,--gtf <gtf_file> Genes annotation file in .gtf format (absolute path)
To generate the input files for visualizing the reconstruction threads go to decoil.
To access all features of decoil-viz, e.g. specify the plot-window, check Documentation
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
Decoil-viz is distributed under BSD-3-Clause license. See LICENSE for details.
Decoil-viz and the content of this research-repository (i) is not suitable for a medical device; and (ii) is not intended for clinical use of any kind, including but not limited to diagnosis or prognosis.