16S from shot gun metagenomes

Theory behind mothur
1

Hey all

Just a general question (I thought this was the best forum to post in).

What do you recommend for looking at 16S sequences parsed out of a shotgun metagenome? Since the sequences wont necessarily overlap they cant be aligned. Is there still a way to compare them to a pyrotag 16S library? Im thinking along the lines of a pCOA plot rather than a OTU analysis.

Anyways, any ideas would be much appreciated

later days

2

So first of all, any analysis method can be presented in PCoA - it’s just a way to visualize data.

I’d be curious to hear other people’s thoughts, but I would suggest a classification/phylotype-based approach interepreted at a very broad level (e.g. phylum or class).