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Krona visualization tool

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.

License

Krona is free to use and open source. It is provided under its own license.

Available

  • Puhti: 2.8.1

Usage

To 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:

sample1.tsv
#queryID  #taxID  #score
query1    9606    0.9
query2    9534    0.8

can be visualized with the command:

ktImportTaxonomy sample1.tsv

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

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

The Krona visualizations are based on HTML5. To study them, you can open a virtual desktop in Puhti web interface and open a browser there.

Alternatively, you can copy these files to a publicly accessible data bucket in Allas, and study the results with your local web browser. You can use commands a-flip or a-publish to do the copying:

For example the command:

a-flip KronaReport.html

will produce a URL that you can copy to your 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). On Puhti, you may also be interested to use ktImportDiskUsage to visualize how many different datasets use space in your directories.

More information