Is It a Necessity to Remove Human Data from Samples for Metagenomic Analysis?

Question

[gtasource]

We have some metagenomics shotgunning data we are looking to analyze with metaphlan2. Looking at the biobakery pipeline, they have you use kneaddata for trimming and removal of human contaminants, before moving on to the actual analysis. My question is, how much of a necessity is it to remove these human contaminants?

[GenoMax]

What do you think? Having human contamination in your metagenomic data is not going to be good.

One option to take care of this: http://seqanswers.com/forums/showthread.php?t=42552

[WouterDeCoster]

Hi gtasource,

Please don't delete a question after somebody helped you. That's not very respectful.

Thanks,
Wouter