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 or MashMap v2.0 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.

Or you can deploy your own instance with the help of the installation documentation.

Documentation

Full documentation, including code API, is available here.

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 of the Genotoul platform (INRAE).