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.
This will run dgenies in standalone mode with Linux and OS X. With Windows, please use Linux through WSL
- First, install conda (once).
- Then, install D-Genies (also once):
conda create -c conda-forge -c bioconda -n dgenies dgenies
- Finally, run D-Genies:
conda activate dgenies
dgenies run
D-Genies will open a browser window. It, can be stop by hitting Ctrl + C in terminal
You can use the demo instance hosted at genotoul.
Or you can deploy your own instance with the help of the installation documentation.
Full documentation, including code API, is available here.
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
D-Genies is developed by the Bioinfo team of the Genotoul platform (INRAE).