taxburst 0.1.8

sunburst plots for taxonomy

taxburst: sunburst charts for taxonomy, based on Krona

WARNING: alpha mode software. Use at your own risk.

This is an update of Krona, written with the following goals in mind:

• liberate tax displays from the tyranny of NCBI taxonomy IDs and taxdump;
• support dynamic generation of Krona-style plots;
• rewrite in modern Python;
• support ~nicer multi-stage generation of XHTML;
• probably other things;

The output HTML is derived from Krona, https://github.com/marbl/Krona.

All bugs are mine until proven otherwise.

Please file bugs and feature requests on the issue tracker.

Examples

Here are some examples of (interactive!) taxburst plots:

• small.tax.html - a small example from sourmash.
• SRR606249.x.podar.tax.html - sourmash taxonomy on the SRR606249 defined community.
• SRR11125891.SingleM.html - displaying the results of singlem pipe on SRR11125891, a pig gut microbiome.
• SRR11125891.summarized.html - sourmash taxonomic breakdown on SRR11125891.
• SRR11125891.tax_annotate.html - genome-resolution taxonomic breakdown of SRR11125891.

A screenshot:

Install

pip install taxburst

Example command lines

All data files are available in the GitHub repository under examples/.

Using sourmash tax metagenome output - summary_csv format

An example using the summary_csv format from sourmash tax metagenome (see tax metagenome docs),

taxburst examples/SRR11125891.summarized.csv \
    -o pages/SRR11125891.summarized.html

then open pages/SRR11125891.summarized.html in a browser.

Using sourmash tax annotate output

An example using the with-lineages format from sourmash tax annotate (see tax annotate docs

taxburst -F tax_annotate \
    examples/SRR11125891.t0.gather.with-lineages.csv \
    -o pages/SRR11125891.tax_annotate.html

then open pages/SRR11125891.tax_annotate.html in a browser.

Using singleM pipe output

An example using the profile format from singlem pipe (see singlem pipe docs):

taxburst -F singleM \
    examples/SRR11125891.singleM.profile.tsv \
    -o pages/SRR11125891.singleM.html

then open pages/SRR11125891.singleM.html in a browser.

Background and history

Krona is a super cool way to explore taxonomic breakdowns of metagenomes. But it's kind of old, and isn't being actively maintained. Moreover, it doesn't work easily with GTDB or other non-NCBI taxonomies.

So, why not grab the JavaScript code and rewrite the preprocessing code?

Voila! 'taxburst'!

I'd call it Krona2 or something, but the licensing for Krona prohibits that, to my understanding. Hence, 'taxburst'.

Miscellaneous notes on input formats

• the sourmash tax annotate format supports assignments down to the genome level, while sourmash tax metagenome's csv_summary format only goes down to the species level.

Citation information

When using taxburst, please cite the Krona paper: Interactive metagenomic visualization in a Web browser, Ondov et al., 2011.

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CTB July 2025

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