MapOptics

MapOptics visualizes Bionano optical mapping data and hybrid scaffolding alignments to support refinement of genome assemblies by extending and ordering scaffolds through alignment against genomic maps.

Key Features:

• Bionano optical mapping visualization: Renders Bionano optical mapping data to display label patterns and map structures.
• Hybrid scaffolding alignment display: Presents alignments between sequence scaffolds and Bionano genomic maps for inspection of scaffold-map correspondences.
• Genome assembly refinement support: Facilitates identification of scaffold extensions and ordering by showing scaffold-to-map alignments used in hybrid scaffolding.
• Performance for large datasets: Provides a fast visualization pathway intended for exploration of large optical mapping datasets as an alternative to more cumbersome analysis programs.

Scientific Applications:

• Genome assembly refinement: Assists in final-stage assembly tasks by enabling visualization-based assessment of scaffold extension and ordering against genomic maps.
• Structural genomics and variation investigation: Supports examination of large-scale genomic structure and potential structural variation through inspection of map–scaffold alignments.

Methodology:

Implements visualization of alignments between sequence scaffolds and Bionano genomic maps; implemented in Java 1.8.