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Old 04-11-2017, 08:54 AM   #4
Senior Member
Location: CT

Join Date: Apr 2015
Posts: 243

I pretty strongly recommend using mothur which aligned the reads to a know database (more robust to discard seqs that don't align rather than picking an arbitrary length). But, know that the illumina 16s kit produces not great results because you have so little overlap to correct miscalled bases.
Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
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