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

Join Date: Apr 2015
Posts: 242
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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 https://github.com/krmaas/bioinforma...r/mothur.batch
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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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