Krona Compare

post by jefftk (jkaufman) · 2024-07-20T01:10:03.994Z · LW · GW · 0 comments

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Cross-posted from my NAO Notebook.

When trying to understand how metagenomic samples differ I often want to drill down through the taxonomic hierarchy, comparing relative abundances. I've tried several tools for this, existing and custom, and haven't been all that happy with any. For most purposes, the tool I like most is Krona, which shows an interactive chart. For example, here's Krona showing the results of running the NAO's v1 metagenomic sequencing pipeline on the unenriched Hyperion Treatment Plant samples from Rothman et al. 2021:


(interactive version)

What I often wish I had, however, are linked Krona charts, where I could see multiple samples at once, and drilling down in one sample showed the corresponding portion of the other samples. After failing to find something like this, I hacked something together by monkey-patching the output of Krona. Here's it comparing the samples from several wastewater treatment plants in the same study:

When I click on "viruses" in any of the plots, all four zoom in on the viral fraction:

That's a lot of Tobamovirus!

I only just made this, so it's likely buggy, but if that doesn't put you off you're welcome to give it a try. The interactive version of the charts above is here (warning: 60MB) and the generation code is open source, on github.


If you're interested in the technical details of how I made this:

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