title: LayerCake: a tool for the visual comparison of viral deep sequencing data.
abstract: BACKGROUND
  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.
  
  
  METHODS
  Program downloads and detailed instructions are available at http://graphics.cs.wisc.edu/WP/layercake under a modified MIT license. LayerCake is a cross-platform tool written in the Processing framework for Java.
  
  
  BACKGROUND
  mcorrell@cs.wisc.edu.
authors.affiliation: Department of Computer Sciences and.
authors.forename: Michael
authors.initials: M
authors.lastname: Correll
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Madison, WI 53706, USA.
authors.forename: Adam L
authors.initials: AL
authors.lastname: Bailey
authors.affiliation: Department of Computer Sciences and.
authors.forename: Alper
authors.initials: A
authors.lastname: Sarikaya
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Madison, WI 53706, USA.
authors.forename: David H
authors.initials: DH
authors.lastname: O'Connor
authors.affiliation: Department of Computer Sciences and.
authors.forename: Michael
authors.initials: M
authors.lastname: Gleicher
mesh_terms: D003196:Computer Graphics; D014644:Genetic Variation; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D012984:Software