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D-Genies
--------

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and WEB application performing large genome alignments using [minimap2](https://github.com/lh3/minimap2) software package and generating interactive dot plots. It enables users to sort query sequences along the reference , zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy to install open source software package (GPL) developed in Python and JavaScript.

How to use?
-----------

You can use the demo instance [here](http://dgenies.toulouse.inra.fr).

Or you can install your own instance. The install documentation is available [here](http://dgenies.toulouse.inra.fr/install).

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Documentation
-------------

Full documentation, including code API, is available [here](https://dgenies.readthedocs.io/en/latest/index.html).

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How to cite?
------------

Cabanettes F, Klopp C. (2018) D-GENIES: dot plot large genomes in an interactive, efficient and simple way. PeerJ 6:e4958 https://doi.org/10.7717/peerj.4958

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Credits
-------

D-Genies is developed by the [Bioinfo team](http://bioinfo.genotoul.fr/index.php/about-us/) of the [Genotoul platform](http://www.genotoul.fr/) ([INRA](http://www.inra.fr/)).