How can we use QIIME2 artifacts for Krona?

Hello again,

Im new to bioinformatics, so i have just found Krona tool. I loved the graphs but i have not found a way to use qiime2 artifacts for this. Seems like there was a way to use biom files from qiime but with qiime2 nobody put much attention for this work. I have found an old topic about this but it died without a solution, so im bringing this up again if someone knows a way.

Also, something Krona-like could work for me, if you know a tool that would generate interactive graphs like Krona, please share with me.

Thank you…

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Yeah, I was on that last thread. Looks like noone make a plug-in yet.

But… this is exactly the “export, convert, graph” workflow I mentioned last time!


And it looks like Calypso now supports Qiime 2, so that’s worth trying.
http://cgenome.net/wiki/index.php/Calypso

Let us know what you find!
Colin

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This may be a really round about way to do it, but I used the OTU table that is generated, opened it in excel, sorted the OTUs by abundance, and just manually entered them ( I only needed top 20 per sample). A workflow would be really nice to have.

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i have seen AmpliSeq but i couldnt find krona_qiime.py in the files. is something wrong with me?
i will definitely check Calypso, thank you.

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I have tried Calypso with different methods, so let me inform you about how far i could go.

First time, I tried Calypso with NCBI taxonomy file. It didn’t parse. Something like unassigned taxa was the result.

Then, I suspected if it was configured to work with some other database since i could get results with ncbi taxonomy file (like taxa bar plots were looking like what i expected) but Calypso didnt work. So i tried it with greengenes database and this time it seems like it worked but i have problems.

Problem one is it doesnt show level 7 (species). There are seven layers, seven levels but while parsing the data it added something before level 1 (kingdom) and species are lost.

Problem two is i had eleven samples. Krona doesnt show them seperately, i guess it got all of them summed up. Is there a way to make it work for each sample seperately?

http://cgenome.net:8080/tempf/sec//calypso-1419774803014512831.session/calypso-9019083894549620338.html?dataset=0&node=0&collapse=false&color=false&depth=7&font=12&key=true

This is the link to the Krona plot i got. Hope someone could help me because i really want an interactive plot like Krona.

Thank you…

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Hello again,
Is it okay to use level-7.csv file in taxa bar plot to generate krona plots? I have managed transforming level-7.csv to a .tsv file that krona would like instead of using feature tables, but I’m not sure of the way since nobody mentioned it before.
Did I do good or something absurd? If my solution is acceptable, I can share the script to save others from trouble.

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Yes, this sounds like a good use case!

Well done. I'm glad you spent the time to get this working. Any advice you have to share with other is very helpful. You might even consider writing a tutorial about :qiime2: -> Krona!

Colin

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Oh, I will be glad to contribute to the community. I just need a week or so, I’m a bit overloaded now :slight_smile: .
Thank you @colinbrislawn

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Hi!
Just wondering if you could share how you got krona to work… really struggling with it and I also couldn’t find krona_qiime.py ! Its a shame because I really like the plots.
Thanks,
Annabelle

krona-argparsed-v5.py (1.7 KB)

This is the last version that I use. This particular one takes input collapsed table and outputs krona.html.

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Hi,
I’m using something very similar to Krona (it produces similar plots) called GraphIan (https://huttenhower.sph.harvard.edu/graphlan).

You just need to get .csv file from QIIME taxonomic bar plot file, and do very minimal editing (such as replacing the “;” with “.”). If you’re interested, I can PM you the details and an example of a plot I generated.

Best :slight_smile:

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Thank you for bringing this tool to my attention! If I can’t get Krona to work soon I will definitely give this a try :grin:

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Thank you - will give it a try!