Krona

Overview

Krona produces interactive, multi-layered pie charts for exploring hierarchical taxonomic classifications in a web browser. It takes tabular taxonomic data (such as Kraken2 or Bracken reports) and generates a self-contained HTML file where users can zoom into any taxonomic level, view proportions, and search for specific taxa. Krona visualisations are widely used to communicate the composition of metagenomic samples in publications and presentations.

Installation

mamba install -c bioconda krona

After installation, update the NCBI taxonomy database used by Krona:

ktUpdateTaxonomy.sh

Basic Usage

Convert a Kraken2 report to Krona input format and create an interactive HTML visualisation.

# Convert Kraken2 report to Krona format
kreport2krona.py -r report.txt -o krona_input.txt

# Create interactive visualization
ktImportText krona_input.txt -o krona_report.html

The resulting krona_report.html can be opened directly in any web browser.

To visualise multiple samples in a single chart:

kreport2krona.py -r sample1_report.txt -o sample1_krona.txt
kreport2krona.py -r sample2_report.txt -o sample2_krona.txt
ktImportText sample1_krona.txt sample2_krona.txt -o combined_krona.html

Key Parameters

Flag / option	Description
`-r` (kreport2krona.py)	Input Kraken2 or Bracken report file.
`-o` (kreport2krona.py)	Output file in Krona-compatible tab-delimited format.
`-o` (ktImportText)	Output HTML file name.
`-n` (ktImportText)	Name for the root node of the chart.
`-q` (ktImportText)	Column number for the query count (default: first column).

Expected Output

krona_input.txt – intermediate tab-delimited file with read counts and taxonomic lineage columns.
krona_report.html – self-contained interactive HTML file. The visualisation shows a hierarchical pie chart where each ring represents a taxonomic level (domain, phylum, class, order, family, genus, species). Users can click to zoom into any taxon and use the search box to highlight specific organisms.