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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

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.



Operational Taxonomic Units (OTUs)

  Defining and interpreting OTUs
  Mapping reads to OTUs
  Closed-reference OTUs
  Problems with closed- and open-reference OTUs
  OTU accuracy
  How to compare two sets of OTUs
  How to make OTUs from different studies or sequencing runs
  Spurious OTUs in mock and real samples
  USEARCH, fast search by global alignment
  UBLAST, fast search by local alignment
  UPARSE, OTUs from next-gen amplicon reads
  UNOISE, denoise / error-correction for amplicon reads
  UPARSE-REF, amplicon read parsing by parsimony
  SEARCH_16S, find 16S rRNA genes in chromosomes and contigs
  SINAPS, predict traits from 16S sequence
  UCLUST, general-purpose sequence clustering
  UCHIME, chimera search
  UCHIME2, improved chimera search
  UNBIAS, correct abundance bias in OTU table
  UNCROSS2, detect and filter cross-talk in OTU table
  Closed-reference OTUs
  RDP Naive Bayesian Classifier