VIVA

VIVA visualizes and analyzes genomic variation from Variant Call Format (VCF) files to support quality control and exploratory analysis of high-throughput sequencing data.

Key Features:

• VCF support: Processes Variant Call Format (VCF) files as the primary input for variant data.
• Variant visualization: Produces visual representations of genomic variation to facilitate assessment of variant calls.
• Quality control and exploratory analysis: Provides visualization outputs suited for quality control, exploratory analysis, and data interpretation of high-throughput sequencing variant datasets.
• Publication-quality graphics: Generates high-quality graphical outputs intended for scientific presentation and publication.
• Consolidation of existing tool functionality: Consolidates functionalities from multiple existing variant visualization tools.
• High-dimensional data handling: Designed to handle high-dimensional genomic variant data typical of large sequencing studies.
• Implementation library: Implements visualization and analysis routines using the VariantVisualization.jl Julia package.

Scientific Applications:

• Quality control of sequencing data: Visualize variant data for quality assessment of high-throughput sequencing experiments.
• Exploratory variant analysis: Investigate patterns and distributions of genomic variants across samples or genomic regions.
• Data interpretation and dissemination: Produce figures and visual summaries to support interpretation and communication of variant analysis results.

Methodology:

Processes Variant Call Format (VCF) files and implements visualization and analysis routines using the VariantVisualization.jl Julia package to generate graphical outputs.