decoil-viz

Visualize ecDNA reconstruction threads and summarize all the results generated by decoil.

• Getting started using docker or singularity
• Decoil-viz configuration
• Citation
• License

Getting started using docker or singularity

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).

Install

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

Run decoil-viz

With docker:

decoil-viz --docker --coverage <coverage_file> --summary <summary_file> --reference <reference_file> --annotation-gtf <gtf_file> --bed <bed_file> --links <links_file> --outputdir <output_directory> --name <output_name>

With singularity:

decoil-viz --singularity --coverage <coverage_file> --summary <summary_file> --reference <reference_file> --annotation-gtf <gtf_file> --bed <bed_file> --links <links_file> --outputdir <output_directory> --name <output_name>

Run test example on your machine

To run a test example go to Example.

Install from source

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

Decoil-viz configuration

Commandline usage:

Usage: decoil-viz [--docker|--singularity|--version|--help] --coverage <coverage_file> --summary <summary_file> --reference <reference_file> --annotation-gtf <gtf_file> --bed <bed_file> --links <links_file> --outputdir <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,--outputdir <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,--annotation-gtf <gtf_file>          Genes annotation file in GTF format (absolute path)

Optional parameters:
  --genes-file [gene_names_file]                Gene names used for filtering the GTF file
  --window-file [window_file]                   BED like file format with the region of interest
  --extend-allowed-chr [anno_list]              List of additional chromosomal annotation (e.g. chrTest,NC_060942.1...)

To generate the input files for visualizing the reconstruction threads go to decoil.

Documentation for advanced users

To access all features of decoil-viz, e.g. specify the plot-window, check Documentation

Citation

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

License

Decoil-viz is distributed under BSD-3-Clause license. See LICENSE for details.

Disclaimer

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.