Bracken Taxonomic Level

[austenrowell]

Hello,

I am using Bracken for a metaviromic analysis. A few of the viruses are showing in my kreport above my threshold of 10, but when I run bracken they are not showing in the breport. When I look at my kreport it shows a -- at the taxonomic level for these viruses although they should be species. When I look in the database at the ktaxonomy.tsv file it lists the virus as S1.

I am wondering if there is a command or argument where bracken will let me see all reads above my threshold or if there is a file I can tweak that will allow these viruses to be called at a species level and appear in the breport.

Thank you for any help and advice! -Austen

[jenniferlu717]

If you want those specific viruses to appear at species level, i think you can change their parent label to G1 and change their levels to S. That may be the easiest to include them without breaking Bracken