D-GENIES: dot plot large genomes in an interactive, efficient and simple way

PeerJ. 2018 Jun 4;6:e4958. doi: 10.7717/peerj.4958. eCollection 2018.

Abstract

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 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. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

Keywords: Dot plot; Genome assessment; Interactive user interface; Large genomes.

Grant support

This work was supported by the France Génomique National infrastructure (funded as part of Investissement d’Avenir Program managed by Agence Nationale pour la Recherche, contract ANR-10-INBS-0009). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.