Definition
Krona is an interactive visualization tool for exploring the composition of metagenomes within a Web browser.
Introduction
Much of the research performed in metagenomics is exploratory, making visualization a prominent aspect of the field. Graphically representing a metagenome, however, is not a trivial task. A single sample can easily contain too many species to represent in one figure, and classifications are not always specific. This often forces visualizations to summarize the sample at higher ranks, such as genus or family, trading details for a meaningful overview. Though user interaction can typically reveal more specific classifications, there is still a trade-off between comparing the most abundant organisms and viewing their most specific classifications (Huson et al. 2007; Meyer et al. 2008). Krona uses multilevel pie charts to visualize both the most abundant organisms and their most specific classifications (Fig. 1). Rather than hiding lower ranks in its...
This is a preview of subscription content, log in via an institution to check access.
Abbreviations
- BLAST:
-
Basic Local Alignment Search Tool
- HTML:
-
HyperText Markup Language
- NCBI:
-
National Center for Biotechnology Information
- RDP:
-
Ribosomal Database Project
- XML:
-
eXtensible Markup Language
References
Draper G, Livnat Y, Riesenfeld R. A survey of radial methods for information visualization. Vis Comput Graph IEEE Trans. 2009;15(5):759–76.
Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007;17(3):377–86.
Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, et al. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386.
Shneiderman B. The eyes have it: a task by data type taxonomy for information visualizations. Visual languages, 2002.
Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol. 2010;6(2):e1000667.
Acknowledgments
This publication was developed and funded under agreement no. HSHQDC-07-C-00020 awarded by the US Department of Homeland Security for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Homeland Security. The Department of Homeland Security does not endorse any products or commercial services mentioned in this publication.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media New York
About this entry
Cite this entry
Ondov, B.D., Bergman, N.H., Phillippy, A.M. (2013). Krona: Interactive Metagenomic Visualization in a Web Browser. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_802-1
Download citation
DOI: https://doi.org/10.1007/978-1-4614-6418-1_802-1
Received:
Accepted:
Published:
Publisher Name: Springer, New York, NY
Online ISBN: 978-1-4614-6418-1
eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences