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Updated: Oct 19, 2025

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Viola: a structural variant signature extractor with user-defined classifications.

Itsuki Sugita1,2, Shohei Matsuyama2, Hiroki Dobashi2

  • 1Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 1130033, Japan.

Bioinformatics (Oxford, England)
|September 17, 2021
PubMed
Summary
This summary is machine-generated.

Viola is a new Python package for analyzing structural variant (SV) signatures in genomes. It aids in classifying, merging, and annotating SVs, demonstrating utility in cancer genomics research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Structural variants (SVs) are large-scale DNA variations implicated in diseases like cancer.
  • Accurate analysis of SVs is crucial for understanding disease mechanisms and developing targeted therapies.
  • Existing tools may lack comprehensive functionalities for SV signature analysis and annotation.

Purpose of the Study:

  • To introduce Viola, a Python package designed for structural variant signature analysis.
  • To provide utilities for custom SV classification, merging multi-SV-caller outputs, and SV annotation.
  • To demonstrate Viola's capability in extracting biologically meaningful SV signatures from cancer genomics data.

Main Methods:

  • Development of a Python package, Viola, offering SV signature analytical functions.
  • Implementation of utilities for custom SV classification and merging of SV caller outputs.
  • Evaluation of computational time for SV annotation using Viola.

Main Results:

  • Viola successfully extracts biologically meaningful structural variant signatures from public cancer genomics data.
  • The package facilitates custom classification, merging, and annotation of structural variants.
  • Computational efficiency of SV annotation using Viola was assessed.

Conclusions:

  • Viola is a valuable tool for structural variant signature analysis in genomics.
  • The package enhances the ability to classify, merge, and annotate SVs, aiding cancer research.
  • Viola provides an efficient and effective solution for SV analysis in large-scale genomic datasets.