What does the tail <1% each taxon mean in the Kaiju output?
This option allows users to exclude rare lineages which would congest the plot. However, underlying analysis is not affected and the data can be replotted.
Can I use the GTDB database within Kaiju?
Yes, you can run the our GTDB-tk Classify app on the same data as you run through Kaiju and compare. The GTDB-tk app is in the Microbial Communities section of the Apps Panel in the Narrative interface. One distinction: Kaiju runs on raw sequencing data (reads) and GTDB-tk works on assembled contigs.
Does the Kaiju analysis give a text output that can be used in R, for example?
Yes, at the bottom of the App cell you can see an option to download kaiju_classification.zip and kaiju_summaries.zip which both contain text files.