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Should I use kneaddata in the following condition?

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?



It is recommended to run Kneaddata quality control step before moving on to downstream analysis and profiling(MetaPhlAn 3.0 and HUMAnN 3.0). It is easier to remove the host contaminant reads using Kneaddata (see more details here on how to use bowtie2 using Kneaddata).

Also, additional information on kneaddata available here,


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