Does that do what uyou're looking for?

Possible 😅 What is meatn with “Please note that abundances above the selected rank are simply ignored. No attempt is made to redistribute those down to the desired rank.” If I choose for example to count at Genus level will it remove counts on higher levels like in Family or Order? (Thats my current problem with Bracken, it redistributes reads at given taxonomic level but removes all information about unclassified and higher Rank counts)

I am also unsure now I read it... @moritz?

What I meant to express is that it does not do the redistribution that Bracken does. But it only sums up reads from lower ranks and would not return abundances of higher ranks.

Yes Im usually using phyloseq for that but was looking for an alternative. So lets say I choose Genus leves, all the counts on higher levels like Family wont be shown in the final file?