Ribbon

Ribbon visualizes genomic alignments of short reads, long reads, and assembled contigs relative to reference genomes to support interpretation and curation of structural variants.

Key Features:

• Alignment visualization: Displays alignments in both reference and read coordinates to show how reads and contigs map relative to a reference genome.
• Structural variant support: Represents read evidence for structural variants (SVs) to aid assessment of SV calls and their supporting alignments.
• Contig and genome-to-genome comparisons: Visualizes contig alignments for genome-to-genome comparisons and comparative genomic analyses.
• File inputs and configurable parameters: Accepts bedpe variant records and BAM alignment files and exposes configurable parameters for read retrieval and visualization.
• Automated variant traversal: Automatically iterates through variants specified in bedpe files to capture multi-read views and selected reads for each variant.
• Memory management and read retrieval: Uses configurable margin parameters around variant coordinates to control which reads are pulled and to limit memory usage during data import.

Scientific Applications:

• Structural genomics: Supports analysis of structural variation by showing read-level evidence for complex SVs.
• Structural variant curation: Facilitates evaluation and curation of SV calls by integrating bedpe variant coordinates with BAM alignments.
• Genome assembly validation: Enables inspection of assembled contigs against reference genomes to validate assembly continuity and alignments.
• Comparative genomics: Provides visualization for contig alignments in genome-to-genome comparisons to assess structural differences between assemblies.

Methodology:

Parses BAM alignments and bedpe variant records to position short reads, long reads, and assembled contigs in both reference and read coordinates, supports contig alignments for genome-to-genome comparisons, iterates bedpe entries to collect multi-read views and selected reads, and applies configurable margin parameters when retrieving reads to limit memory usage.