D-GENIES : Dot plot large GENomes in an interactive, efficient and simple way

Plateforme Bio-informatique, Toulouse Genopole, Institut National de la Recherche Agronomique, Castanet-Tolosan, France
DOI
10.7287/peerj.preprints.26567v1
Subject Areas
Bioinformatics, Genomics, Computational Science
Keywords
dot plot, genome assessment, interactive user interface, large genomes
Copyright
© 2018 Cabanettes et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Cabanettes F, Klopp C. 2018. D-GENIES : Dot plot large GENomes in an interactive, efficient and simple way. PeerJ Preprints 6:e26567v1

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/.

Author Comment

This is a preprint submission to PeerJ Preprints.