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Related Experiment Video

Updated: Jan 6, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing.

Davide Bolognini^1,2, Ashley Sanders³, Jan O Korbel³

¹Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy.

Bioinformatics (Oxford, England)

|October 8, 2019

Summary

This summary is machine-generated.

VISOR enables haplotype-specific simulations of structural variants (SVs) for various ploidy levels and sequencing types. This versatile tool aids in simulating complex genomic data, including cancer heterogeneity, at high resolution.

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Accurate simulation of structural variants (SVs) is crucial for understanding genomic diversity and disease.
Existing tools often lack the flexibility to simulate haplotype-specific SVs across different ploidy levels and sequencing data types.

Purpose of the Study:

To introduce VISOR, a novel tool for haplotype-specific simulation of simple and complex structural variants.
To provide a versatile platform for simulating bulk and single-cell sequencing data with SVs at single-basepair resolution.

Main Methods:

VISOR implants SVs into FASTA haplotypes with optional nearby single-nucleotide variants.
It simulates short or long reads from these haplotypes using standard error profiles, supporting double- or single-stranded data.
The tool generates haplotype-tagged BAM files and includes interactive visualization methods for simulated variants.

Main Results:

VISOR offers unparalleled versatility in simulating SVs compared to existing tools.
It successfully generates haplotype-resolved genomic data, including complex structural variants.
The tool supports simulations for haploid, diploid, and higher ploidy data, applicable to both bulk and single-cell sequencing.

Conclusions:

VISOR provides a robust and versatile platform for simulating haplotype-specific structural variants.
It lays the foundation for simulating complex, haplotype-resolved cancer heterogeneity data.
The tool's capabilities advance genomic data simulation for research in various biological contexts.