D-GENIES

D-GENIES performs large-genome pairwise alignments using minimap2 and visualizes alignments as interactive dot plots to facilitate detection of structural variants such as repetitions, breaks, and inversions.

Key Features:

• Large-genome alignment: Uses minimap2 to compute efficient alignments of substantial genomic sequences.
• Interactive dot-plot visualization: Generates dot plots that highlight repetitions, breaks, and inversions in genome comparisons.
• Query sorting along reference: Allows ordering of query sequences against a reference genome to clarify correspondence between chromosomes or scaffolds.
• Implementation: Implemented using Python and JavaScript.

Scientific Applications:

• Evolutionary biology: Visualizes genome rearrangements and structural variants to support inference of evolutionary events.
• Comparative genomics: Performs detailed comparisons of large genomes through alignment visualization to identify structural differences.
• Bioinformatics research: Supports analyses that require large-scale sequence alignment and structural-variation assessment.

Methodology:

Alignments are computed with minimap2 and rendered as interactive dot plots; query sequences can be sorted relative to a reference; the software is implemented in Python and JavaScript.