Hi @franzosa @fbeghini !!!
I have profiled shotgun data with MetaPhlAn 3.0 with
--ignore_eukaryotes --ignore_archaea. The output abundance now will be used as input of HUMAnN 3.0. In this context, should I use Kneaddata before the MEtaPhlAn step? Can’t I directly use the metagenome sequences as input for HUMAnN and MetaPhlAn without the Kneaddata step? Will not HUMAnN be able to discard the host reads?