Kraken2 output visualisation with Krona Viruses not shown
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22 days ago

Dear all, I am trying to visualize my kraken2 output with Krona and the results look very doubtful. I build a metagenomic pipeline with multiple filtering steps and I should have mainly viral sequences (a brief look into my kraken2 output files confirms this). However the Krona output displays around 50% bacteria and 50% "other root". I am sure this is a very silly mistake on my part somewhere but I cannot figure it out... I used this guide: https://genomics.sschmeier.com/ngs-taxonomic-investigation/index.html to install and run Krona and on the surface it seems to work but the output is definitely wrong. Here is an example of my command when running:

$ ktImportTaxonomy file_kraken2_output.txt
Loading taxonomy...
Importing 20398_20_S19_combined_kraken2_output_report.txt...
   [ WARNING ]  The following taxonomy IDs were not found in the local database and were set to root (if they were recently added to NCBI, use updateTaxonomy.sh to update the local
                database): 588374 2572 990749 3 539464 36 588380 588378 169 377 26 8 15 4 130 29676 208 73 401669 12 5 135 390
Writing taxonomy.krona.html...<

I have run "updateTaxonomy.sh" multiple times already and it does not change anything...

Any help would be much appreciated!

Here is an example of the output I get

metagenomics kraken2 krona virus • 265 views
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In your query, there are two issues:

  1. Krona is not drawing viruses though it is present in kraken2 ouptut
  2. Kraken2 output doesn't have viruses.

If 1st one is the issue, please post kraken2 output with virus entries.

If 2nd one is the issue, you need to post what databases you have used in classification and if reference database used in kracken2 contain viral entries or not.

My guess is that you have later issue i.e issue with Kracken2, not with krona. Check the reference databases used in kracken classification.

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Thank you for your reply, sorry I missed it the last couple of days!

I have attached a screenshot of my kraken2 output to prove that there is virus in there so I do think its an issue with Krona after all...Or am I missing something here?

enter image description here

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data images are not helpful.

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okay, what would be helpful?

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