VISOR

VISOR simulates haplotype-specific structural variants in genomic sequences and generates sequencing reads to support evaluation of variant detection and haplotype-resolved analyses.

Key Features:

• Haplotype-Specific Structural Variant Simulation: Implants simple and complex structural variants into FASTA haplotypes at single-basepair resolution.
• Single-Nucleotide Variant Integration: Optionally introduces nearby single-nucleotide variants (SNVs) to increase realism of simulated genomic datasets.
• Short- and Long-Read Simulation: Generates sequencing reads from modified haplotypes according to standard sequencing error profiles.
• Strand-Specific Data Simulation: Produces simulated datasets representing either double-stranded or single-stranded sequencing data.
• Haplotype-Tagged Alignment Output: Generates haplotype-tagged BAM files for downstream haplotype-aware analyses.
• Variant Visualization: Provides visualization methods for examining simulated variants within generated sequencing data.

Scientific Applications:

• Structural Variant Detection Benchmarking: Generates controlled datasets for evaluating structural variant detection algorithms.
• Haplotype-Resolved Genomics: Simulates haplotype-specific genomic variation for studies requiring phased variant information.
• Cancer Genomics Simulation: Models structural variation patterns and genomic heterogeneity relevant to tumor evolution studies.

Methodology:

VISOR introduces structural variants into FASTA haplotypes at single-basepair resolution, optionally incorporates single-nucleotide variants, generates short and long sequencing reads with sequencing error profiles, and outputs haplotype-tagged BAM files for analysis and visualization.