MARS

MARS refines and detects structural variants (SVs), specifically indels, in haplotype-resolved diploid genome assemblies using linked-read sequencing to enable high-sensitivity genotyping and phasing across multiple samples.

Key Features:

• Haplotype-resolved assembly compatibility: Operates on haplotype-resolved diploid assemblies to call and refine structural variants.
• Multiple alignment-based refinement: Uses a multiple alignment-based approach to define and refine SV calls across multiple samples.
• Linked-reads integration: Integrates linked-read sequencing data to improve sensitivity and accuracy of SV detection and phasing.
• High-sensitivity genotyping and phasing: Provides high-sensitivity genotyping and phasing of SVs across multiple samples.
• Population-wide analysis: Aligns and analyzes SVs across large cohorts to define population-level variant representations.
• Validation against Mendelian inheritance and PacBio HiFi reads: Demonstrated validation rates of 73%–87% for indels in diploid assemblies when evaluated with Mendelian inheritance patterns and PacBio HiFi reads.

Scientific Applications:

• Genomic research: High-resolution SV genotyping and refinement across multiple diploid samples.
• Population genetics: Analysis of SV distribution and refinement at population scale.
• Disease genomics: Identification and phasing of SVs relevant to disease-associated genetic variation.

Methodology:

MARS applies a multiple alignment-based approach that integrates linked-read sequencing data to refine SV detection in diploid assemblies and evaluates detected SVs against Mendelian inheritance patterns with validation using PacBio HiFi reads.