D-GENIES is a tool for comparing large genome assemblies using interactive dot plots. Its name stands for Dot plot large Genomes in an Interactive, Efficient and Simple way.
Dot plots provide a visual representation of sequence similarity between genomes. They are particularly useful for detecting structural differences, including rearrangements, inversions, duplications and regions that fail to align. However, producing useful comparisons can become computationally demanding when working with very large assemblies.
D-GENIES combines genome alignment software with a browser-based visualisation interface. Researchers can examine the results interactively, making it easier to investigate similarities and structural differences between assembled sequences.
This is free and open source software.
Key Features
- Generates interactive dot plots for comparing large genome assemblies and individual sequence collections.
- Uses Minimap2 or MashMap to align genome sequences before producing the visualisation.
- Supports importing existing alignments, including PAF and MAF files, rather than requiring every comparison to be calculated again.
- Displays matching regions as graphical alignments, helping identify inversions, repetitions and potential assembly problems.
- Offers interactive zooming and panning to examine selected regions of an alignment in greater detail.
- Allows query contigs to be reordered according to their alignment with the reference genome.
- Supports reversing the orientation of individual contigs when examining the relationship between assemblies.
- Displays alignment coordinates when interacting with matching regions in the dot plot.
- Provides alternative colour palettes and controls for adjusting the visual presentation.
- Exports dot plots as images and generates downloadable alignment and sequence files.
- Can produce a standalone HTML representation of a dot plot for viewing without an active server connection.
- Supports both locally executed analyses and deployment as a shared web service.
Website: github.com/genotoul-bioinfo/dgenies
Support:
Developer: GenoToul Bioinformatics Platform, INRAE
License: GNU General Public License v3.0
D-GENIES is written in JavaScript and Python. Learn JavaScript with our recommended free books and free tutorials. Learn Python with our recommended free books and free tutorials.
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