Hi All,
I would appreciate clarification on whether KneadData is recommended for mouse fecal samples that underwent shotgun metagenomic sequencing. My understanding is that fecal samples generally contain less host DNA than tissue-derived samples, but I’m not sure whether host read removal is still necessary before running MetaPhlAn and HUMAnN. Because KneadData can be computationally expensive at scale, if this step is not essential for mouse fecal metagenomes, we are considering omitting it.
Thanks!
Claire