SVDSS

SVDSS detects structural variants (SVs), specifically insertions and deletions, from low-error long-read sequencing data such as PacBio HiFi by using sample-specific strings to improve discovery in repetitive and diploid genomic regions.

Key Features:

• Hybrid methodology: Combines mapping-free, mapping-based, and assembly-based approaches for SV discovery.
• Sample-specific strings: Derives and uses sample-specific strings from accurate long-read sequencing data to identify variant signals.
• Sequencing support: Operates on low-error long reads, explicitly including PacBio HiFi data.
• Variant types: Detects insertion and deletion structural variants.
• Performance in complex regions: Targets repetitive and hard-to-call genomic regions and addresses challenges from the diploid nature of the genome.
• Comparative advantage: Demonstrates improved calling accuracy over state-of-the-art mapping-based methods on PacBio HiFi reads for insertions and deletions.

Scientific Applications:

• Human genomics: Discovery of structural variants in human samples, including regions with high sequence variability.
• Repetitive and hard-to-call regions: Improved detection of insertions and deletions within repetitive genomic loci and other challenging regions.
• Precision medicine and genomic analyses: Supports SV discovery relevant to genetic diversity studies and precision medicine applications.

Methodology:

Combines mapping-free, mapping-based, and assembly-based computational approaches and uses sample-specific strings derived from PacBio HiFi long reads to identify insertion and deletion SVs.