Table of Contents

Krona visualization tool

Description

Krona is a visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming.

Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with any modern web browser.

Version

  • Krona 2.7.1 is available in Puhti

Usage

To take in use KronaTools commands, load the biokit module.

module load biokit

Many bioinformatics tools provide classifications based on the NCBI Taxonomy. These classifications can be imported to Krona via tab-separated files listing taxonomy IDs.

For example file (sample1.tsv)

#queryID  #taxID  #score
query1    9606    0.9
query2    9534    0.8

Can be visualized with command:

ktImportTaxonomy sample1.sv 

The three columns, by default, are query-ID, taxonomy-ID, and score (optional), but these can be changed using options -q,-t, and -s. Commented lines (#) are ignored. For example an output file from Kraken2 can be visualized with command:

ktImportTaxonomy -q 2 -t 3 KrakenOutput -o KronaReport.html

The Krona visualizations are based on HTML5 and thus it is not straight forward to study them in Puhti. However if you copy these files to a publicly accessible data bucket in Allas, you can study the results with your local web browser. You can use commands a-flip or a-publish to do the copying:

For example command:

a-flip KronaReport.html

Will produce a URL that you can copy to you browser.

In addition to ktImportTaxonomy there are several application specific data import tools: For example for BLAST (ktImportBLAST) and MG-RAST (ktImportMGRAST). There are also general purpose tools for text (ktImportText) and XML data (ktImportXML). In Puhti you may also be interested to use ktImportDiskUsage to visualize how much different datasets use space in your directories.

More information