LayerCake

LayerCake visualizes sequence variability, coverage depth, and quality scores from next-generation sequencing (NGS) data to compare viral populations across whole genomes.

Key Features:

• Simultaneous Visualization: Presents variations across entire viral genomes and multiple populations concurrently to reveal patterns of sequence variability.
• Multi-metric Display: Displays coverage depth and per-base quality scores alongside sequence variation across genomes.
• NGS Data Integration: Operates on next-generation sequencing (NGS) data to derive population-level variation.
• Population Structure Comparison: Enables construction and comparison of complex viral population structures by comparing sequence variations.
• Implementation: Implemented in the Processing framework for Java.

Scientific Applications:

• Viral evolution analysis: Identifies and visualizes sequence changes relevant to viral adaptation and evolutionary dynamics.
• Within-host population dynamics: Characterizes intra-host viral population structure and temporal changes.
• Transmission and epidemiology: Compares viral populations across infected individuals to inform transmission pathway analyses.
• Antiviral resistance investigation: Highlights sequence variation relevant to potential resistance to treatments.

Methodology:

Processes NGS data to compare sequence variations and constructs visual representations of population structures, sequence variability, coverage depth, and per-base quality scores.