Qiime2 output to generate Krona charts?

Looking for suggestions on how to use qiime2 data in order to generate Krona charts. I am stuck at exporting a table containing multiple levels of taxonomy/feature. Any help appreciated! Thanks!

2 Likes

I like this idea. I feel like this would be a natural way to view taxonomy and would make a good qiime plugin.
https://github.com/marbl/Krona/wiki

Hey @costam,

Looking at their examples there’s probably not going to be a good way to pull this off without some programming (or a plugin like @colinbrislawn is suggesting).

The information you need is in the FeatureTable[Frequency] and FeatureData[Taxonomy] artifacts, but their format combines these into what looks like a jagged TSV where the abundances are present at each taxonomic level.

This wouldn’t be too hard for a developer to program, but there isn’t really a way to do this as an user of QIIME 2.

Sorry I don’t have better news.

1 Like

Hey @costam,
Just to add to @ebolyen’s advice, I’d recommend getting in touch with the Krona developers — it looks like they have a bunch of different scripts for generating Krona plots from different input formats. Given the QIIME2 formats (or export formats), they may know a way or may be interested in developing a formatter in the future.

Thanks for bringing this up!

1 Like

Hey, I found this script which is designed to turn a .biom table into a Krona plot.
https://github.com/GenomicaMicrob/OTUsamples2krona

Maybe you could export your data from Qiime2, convert your otu.biom file into a otu.txt file, then use that script to get it ready for Krona.

Let us know if you need help along the way.
Colin

Thanks everyone for their input. Colin: I tried doing that (using the script or Calypso) and I am always stuck in generating the “otu table”. As someone said above, I can’t export all levels of taxonomy at once. What’s your suggestion?

Best,
Matheus

I have never used Krona, so I’m afraid I’m not much help here.

Have you considered opening up an issue on the GitHub page and asking the Krona devs for help? The absolute best solution would be for them to make a qiime plugin that ‘just works,’ but that’s more work then doing a single conversion…

On the other hand, the qiime 1 paper has over 3000 citations, so maybe the Krona devs would be interested in contributing to qiime 2!

2 Likes

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.