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Old 06-23-2017, 11:41 AM   #2
Senior Member
Location: CT

Join Date: Apr 2015
Posts: 242

I've only used the Illumina pipeline once (for that matter I prefer mothur to qiime). The Illumina pipeline is a total black box, do you trust every decision they made for you but didn't document? When I used it, it seemed to just be a taxonomic matching against a database (blast? maybe) rather than OTU based

Check out the mothur miseq SOP for guidelines. Feel free to use my batch file which is based on that SOP
Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

Last edited by thermophile; 06-23-2017 at 11:44 AM.
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