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, and have docker engine running, or, 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> --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>

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> --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.

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 pre-print:

Madalina Giurgiu, Nadine Wittstruck, Elias Rodriguez-Fos, Rocio Chamorro Gonzalez, Lotte Bruckner, Annabell Krienelke-Szymansky, Konstantin Helmsauer, Anne Hartebrodt, Richard P. Koche, Kerstin Haase, Knut Reinert, Anton G. Henssen. Decoil: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data. bioRxiv, 2023, DOI: https://doi.org/10.1101/2023.11.15.567169

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.

madagiurgiu25 / decoil-viz

readme