Getting started in 18S analysis

Can some one please suggest me some places where I could read and inform myself about 18S analysis using mothur pipeline.

I am tasked with the analysis of environmental samples belonging to bacteria, fungi, algae, protozoa,…

For bacteria and archea, MiSeq SOP offers an excellent resource for a standard pipeline.
I really would like to know how to approach the eukaryote taxonomy in our data.

Thanks in advance.

It’s really the same SOP. There are SILVA euakryote databases for alignment and classification on the appropriate wiki pages which you need to use instead of the usual ones, but it’s pretty much a matter of swapping your databases and business as usual.

To user: dwaite
I truly appreciate your timely and very helpful response. Thank you very much.