LayerCake: a tool for the visual comparison of viral deep sequencing data.

Motivation: The advent of next-generation sequencing (NGS) has created unprecedented opportunities to examine viral populations within individual hosts, among infected individuals and over time. Comparing sequence variability across viral genomes allows for the construction of complex population structures, the analysis of which can yield powerful biological insights. However, the simultaneous display of sequence variation, coverage depth and quality scores across thousands of bases presents a unique visualization challenge that has not been fully met by current NGS analysis tools. Results: Here, we present LayerCake, a self-contained visualization tool that allows for the rapid analysis of variation in viral NGS data. LayerCake enables the user to simultaneously visualize variations in multiple viral populations across entire genomes within a highly customizable framework, drawing attention to pertinent and interesting patterns of variation. We have successfully deployed LayerCake to assist with a variety of different genomics datasets.