VarBen

VarBen generates customized reference sequencing datasets by editing original next-generation sequencing (NGS) reads to simulate somatic single-nucleotide variants (SNVs), small insertions and deletions (indels), and large structural variants for evaluation and validation of bioinformatics pipelines in clinical oncology.

Key Features:

• Read-level editing: Directly edits original sequencing reads to introduce specified variants into datasets.
• Simulated variant types: Introduces single-nucleotide variants (SNVs), small insertions and deletions (indels), and large structural variants.
• Sequencing platform support: Handles data from Illumina and Ion Torrent sequencing platforms.
• Sequencing scopes: Applicable to targeted panel, exome, and whole-genome sequencing datasets.
• Reference dataset generation: Produces customized reference datasets for pipeline development, validation, and testing.
• Realism/validation: Generates simulated variants that are comparable to real-world sequencing data for reliability assessment.

Scientific Applications:

• Pipeline evaluation: Evaluates and validates somatic variant detection accuracy of bioinformatics pipelines in clinical oncology.
• Local benchmarking: Generates tailored reference datasets to assess pipeline performance on laboratory-specific sequencing data.
• Comparative validation: Enables comparison of simulated variants with real-world data to confirm simulation realism and pipeline reliability.

Methodology:

Edits original sequencing reads to introduce SNVs, small indels, and large structural variants into Illumina and Ion Torrent targeted, exome, or whole-genome datasets, and compares simulated variants with real-world sequencing data.