Chapter 10 Krona plot

Krona is an interactive metagenome species abundance visualisation tool.

10.1 Krona: run

We can use the Kraken2 report files to create our Krona plots. With the below command we can import our Kraken2 taxonomy (within the report file) into a Krona html.

ktImportTaxonomy -o kraken2.krona.html *.kreport2

• -o is our output html file
• The final argument *.kreport2 represents all of our .kreport2 files in the current directory.
  • The * is a wild-card, meaning any characters any number of times. Therefore *.kreport2 identifies the files K1.kreport2 K2.kreport2 and W1.kreport2.

You will get a warning that not all taxonomy IDs were found. We will ignore this but in your own future installations this should be addressed with Krona's updateTaxonomy.sh command.

10.2 Krona: visualise

We can view our interactive chart in a web browser. This shows the percentage of reads that were classified to various taxonomies at different levels.

firefox kraken2.krona.html &

This is an interactive multi-tiered pie chart with many options. Some of the interactivity is described below:

• To choose a sample to view, click on the sample name in the top left.
• To zoom into a lower taxonomy, double click on the taxonomy's name on the pie chart.
  • E.g. double click the word "Bacteria" on the pie chart to zoom into Bacteria and therefore ignore Eukaryota, and "[other Root]".
• To zoom out to a higher taxonomy, click on the taxonomy's name in the middle of the pie chart.
  • E.g. click the word "root" in the middle of the pie chart to zoom back out from any lower level of taxonomy.
• To view percentage stats of a taxonomy, click on the taxonomy name on the pie chart.
  • This will display the percentage this taxonomy covers of all the different taxonomies above it that it belongs to. This is displayed on the right side of the screen.
  • E.g. Click on Pseudomonadota to see the percentage of the Root it accounts for and to see the percentage of Bacteria it accounts for in the sample.

10.3 Krona: MCQs

Viewing the Krona, attempt the below MCQs.

1. What percentage of the root was classified to Bacteria for K1?
   2% 34% 35%
2. What percentage of bacteria was classified to Pseudomonadota for K2?
   2% 34% 35%
3. What percentage of the root was classified to Myxococcota for W1?
   2% 34% 35%
4. What percentage of the Terrabacteria groups was classified to Cellulomonas gilvus for K2?
   39% 8% 6%
5. What percentage of Alphaproteobacteria was classified to Phenylobacterium immobile for K1?
   39% 8% 6%
6. What percentage of Viridiplantae (in Eukaryota) was classified to Parasponia for W1?
   39% 8% 6%