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12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



Tutorials, exercises and example scripts for OTU analysis

OTU analysis example scripts Image
  Minimal OTU pipeline for Illumina unpaired reads
  OTUs and ZOTUs (denoised sequences) from Illumina paired reads
  OTUs and ZOTUs, OTU table, diversity & taxonomy MiSeq 2x250 16S V4 reads
  OTUs and ZOTUs, OTU table, diversity & taxonomy MiSeq 2x300 ITS reads
  OTUs, OTU table, diversity & taxonomy 454 16S V3-V5 reads

Tutorial exercises with solutions
  Mouse gut samples and mock community, 16S 2x250 V4
  Human Microbiome Project samples, 454 reads
  MiSeq 2x250 ITS reads