VVODKA

Versatile Visualisation of Overlapping DNA by K-mer Analysis.

VVODKA is an exhaustive genome dot plotting tool implemented in Python 3.9. It utilizes the matplotlib 3.7.0 library for creating genome dot plots. The tool takes user arguments through the docopt 0.6.2 library and extracts sequences from input FASTA files using pyfastx 0.9.1.

Dependencies

Python 3.9
matplotlib 3.7.0
docopt 0.6.2
pyfastx 0.9.1

You can install these dependencies using pip:

pip install matplotlib==3.7.0
pip install docopt==0.6.2
pip install pyfastx==0.9.1

Install

git clone https://github.com/GijsBakker/VVODKA

Example Data

EMALE04 - 3 viral genomes (25 kbp in size)
Prochlorococcus - 5 bacterial genomes (~2 Mbp in size)
Arabidoptsis - 2 eukaryotic genomes (120-200 Mbp in size)
Cflag_c131 - EMALE intergrated in sequence containing retrotransposon (79KB in size)

Usage

To generate a genome dot plot using VVODKA, you need to provide the following information:

Usage:
    VVODKA.py -k <kmer_size> [-r <dpi>] [-s <self>] [-d <dot_size>] <files>...
    VVODKA.py (-h | --help | --version)

Options:
    -k <kmer_size>  Specify the size of the k-mer
    -r <dpi>        Specify the DPI [default: 600]
    -s <self>       Specify if files should be plotted against themselves, use Y
                    to plot against itself or N to not plot against itself [default: Y]
    -d <dot_size>   Specify the dot size to be used in the dot plot [default: 2]
    <files>...      Specify the files which are plotted against each other

For example, to generate a genome dot plot with a k-mer size of 13, a dpi of 300, and plot the file Cflag_c131.fna against itself, use the following command:

VVODKA.py -k 13 ../../data/PaperData/Cflag_c131.fna

Contact

If you have any questions or feedback regarding VVODKA, feel free to either report issues directly via github or contact g.h.bakker@st.hanze.nl

GijsBakker / VVODKA