MoMI-G

MoMI-G visualizes structural variants in complex genomes using a variation graph framework to represent allelic branches and integrate long-read alignments for detailed inspection of large and nested SVs common in cancer genomes.

Key Features:

• Graph-Based Visualization: Employs a variation graph framework that represents alleles as branches to capture large (> megabase) and nested structural variants beyond linear reference models.
• Multi-Scale View Modules: Provides coordinated views from whole-genome context down to nucleotide-level long-read alignments for multi-scale examination of SVs.
• Simultaneous Alignment Inspection: Displays read alignments spanning both reference and alternative alleles within the same view to reveal support for heterozygous structural variants.
• Interval Card Deck: Enables rapid manual inspection of hundreds of structural variants by pairing identified SVs with supporting long-read alignments and annotations to filter false positives.

Scientific Applications:

• Cancer genomics: Characterizes complex structural variations in cancer genomes, including large and nested SVs relevant to development and progression.
• Long-read sequencing analysis: Integrates long-read alignments and annotations to support validation and interpretation of structural variants detected by long-read sequencing.

Methodology:

Represents structural variants as branches in a variation graph and renders long-read alignments across reference and alternative alleles to visualize SV support as an alternative to linear reference models.