Metadata-Version: 2.1
Name: dgenies
Version: 1.3.0
Summary: Dotplot large Genomes in an Interactive, Efficient and Simple way
Home-page: http://dgenies.toulouse.inra.fr
Author: Floreal Cabanettes
Author-email: floreal.cabanettes@inra.fr
Maintainer: Philippe Bordron
Maintainer-email: philippe.bordron@inrae.fr
License: UNKNOWN
Project-URL: Sources, https://github.com/genotoul-bioinfo/dgenies
Project-URL: Bug Tracker, https://github.com/genotoul-bioinfo/dgenies/issues
Project-URL: Changelog, https://github.com/genotoul-bioinfo/dgenies/blob/main/CHANGELOG.md
Project-URL: Wiki, https://github.com/genotoul-bioinfo/dgenies/wiki
Keywords: bioinformatics,genome,comparison,dotplot,inrae,genotoul
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Web Environment
Classifier: Framework :: Flask
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Programming Language :: JavaScript
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
License-File: LICENSE.txt

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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) or [MashMap v2.0](https://github.com/marbl/MashMap/) software packages 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 hosted at genotoul](http://dgenies.toulouse.inrae.fr).

Or you can deploy your own instance with the help of [the installation documentation](http://dgenies.toulouse.inrae.fr/install).

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

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

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

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/) ([INRAE](http://www.inrae.fr/)).

