LayerCake

LayerCake is a tool created for visualizing viral variation from next generation sequencing data, created as a collaboration between labs associated with UW Computer Sciences and UW Pathology & Laboratory Medicine Departments.

LayerCake is meant to afford the quick analysis of variation over an entire viral genome, and between different viral populations. Questions LayerCake might answer include:

• What regions of the genome of an infecting viral population have the most variation from a reference after long periods of infection?
• For animal populations with different responses to viral infection, how are these different responses reflected in the pattern of variation in the populations of the infecting viruses?
• Over the course of an infection, where and how much do viral populations experience genetic variation?

Explore this site to learn more about the LayerCake tool, and to download LayerCake and associated datasets.

LayerCake was made with Processing, and requires an up to date Java runtime environment.

Current publications associated with LayerCake:

• Visualizing Virus Population Variability From Next Generation Sequencing Data (2011)
• Conditional  CD8+ T Cell Escape during Acute Simian Immunodeficiency Virus Infection (2012)
• High Genetic Diversity and Adaptive Potential of Two Simian Hemorrhagic Fever Viruses in a Wild Primate Population (2014)