NanoSatellite

NanoSatellite characterizes tandem repeats directly from Oxford Nanopore Technologies PromethION raw electric current (squiggle) data to provide accurate measurements of repeat length, motif interruptions, and expanded alleles in disease-associated genomic loci.

Key Features:

• Direct analysis of electric current (squiggle) data: Operates on raw electric current signals produced by Oxford Nanopore sequencing rather than on base-called sequences or alignments.
• Improved accuracy in complex regions: Enhances characterization of GC-rich tandem repeats, expanded alleles, and motif interruptions for more precise repeat length and sequence determination.
• Scalable coverage with PromethION: Demonstrated capability to achieve ~30× human genome coverage with a single PromethION flow cell per individual, enabling analysis of very long repeats such as the ~10,000-base pair ABCA7 VNTR.
• Complementary to existing tools: Provides an alternative approach to Guppy "flip-flop" base caller and tandem-genotypes by addressing limitations in challenging genomic repeat regions.

Scientific Applications:

• Disease-associated repeat analysis: Accurate measurement of tandem repeats implicated in disease, including the Alzheimer's-associated ABCA7 VNTR.
• Genome-wide repeat profiling: Large-scale and population-level surveys of tandem repeat length and composition using PromethION long-read data.
• Characterization of complex repeat architectures: Detection and delineation of GC-rich repeats, motif interruptions, and large expanded alleles that are problematic for base-called workflows.

Methodology:

Applies dynamic time warping to Oxford Nanopore squiggle (raw electric current) data to characterize tandem repeats directly, bypassing base calling and alignment.