LayerCake: a Tool for the Visual Comparison of Viral Deep Sequencing Data

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2015 Jul 9

PMID 26153515

Citations 2

Authors

Michael Correll

Adam L Bailey

Alper Sarikaya

David H OConnor

Michael Gleicher

Affiliations

Soon will be listed here.

Abstract

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.

Availability And Implementation: 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.

Contact: mcorrell@cs.wisc.edu.

Citing Articles

Goldilocks: a tool for identifying genomic regions that are 'just right'.

Nicholls S, Clare A, Randall J Bioinformatics. 2016; 32(13):2047-9.

PMID: 27153673 PMC: 4920124. DOI: 10.1093/bioinformatics/btw116.

Biogenesis, Function, and Applications of Virus-Derived Small RNAs in Plants.

Zhang C, Wu Z, Li Y, Wu J Front Microbiol. 2015; 6:1237.

PMID: 26617580 PMC: 4637412. DOI: 10.3389/fmicb.2015.01237.

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