HumanN3 remove human reads?

Hello @franzosa !

  1. Doubt 1:

I have a doubt, can we use assembled contigs for humann3 input?

  1. Doubt 2:

Also, do I need to run KneadData before running HumanN3?
For running metaphlan3 I did not use kneadData because I thought the chocophlan database has only microbial species markers, it was not necessary to remove human reads. Please let me know if my understanding is not correct. But before running HumanN3 should I run KneadData. If yes why?

  1. Doubt 3:

I had profiled the community using metaphlan3 earlier, now I am planning to do functional annotation of the same datasets, and since they are paired-end data so you have explained in one of the topics that the paired-end files should be concatenated before running humann3 but is that going to change the metagenome community profiling results that I had already obtained by running metaphlan3 for the paired-end files because at that time I did not concatenate the fatsq files?