Chapter 10 Krona

Krona is an interactive metagenome species abundance visualisation tool. We will use it to produce interactive tiered pie charts from our Kraken2 output.

10.1 Import taxonomy

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 Tiered piecharts

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 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%