FaNDOM

FaNDOM aligns Bionano Saphyr optical map molecules and contigs to reference genomes to identify genomic structural variants.

Key Features:

• Seed-Based Filtering: Employs a seed-based filter that reduces the search space during alignment to improve computational efficiency.
• Nested Distance Seeding: Utilizes a nested distance seeding approach to streamline candidate selection for alignments.
• Speed and Efficiency: Demonstrated 4 to 14 times faster runtimes on benchmark human datasets while maintaining comparable sensitivity and specificity.
• High-Coverage Optical Mapping Support: Processes long optical mapping (OM) data exceeding 150 kbp from microfluidic technologies, using single-molecule readouts of fluorescently labeled sequence motifs on DNA fragments resolved to nucleotide-level coordinates.

Scientific Applications:

• Scaffolding for De Novo Assembly: Aligns optical map data to support scaffolding during de novo genome assembly.
• Identification of Structural Variants: Detects deletions, duplications, gene fusions, and gene-disrupting rearrangements, including applications in mapping variants in cancer cell lines.

Methodology:

FaNDOM utilizes a nested distance seeding approach to streamline the alignment process, reducing computational complexity to enable rapid processing of large optical mapping datasets while preserving alignment accuracy.