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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.



What's new in USEARCH v11

See also
What's new in version 10

New features
  Machine learning
  Improved cross-talk detection
  Novel alpha diversity metrics
  Octave plots for visualizing alpha diversity
  Statistical significance of diversity differences between groups
  Cross-validation by identity (CVI)

New commands
  calc_lcr_probs  Calculate lowest common rank probabilities
  cluster_tree  Construct clusters from tree using distance cutoff
  distmx_split_identity  Split distance matrix into test/training pair for CVI
  fastx_syncpairs  Sort forward and reverse reads into the same order
  fastx_trim_primer  Remove primer-binding sequence from FASTx file
  forest_classify   Classify data using random forest
  forest_train  Train random forest classifier
  nbc_tax   Predict taxonomy using RDP Naive Bayesian Classifier algorithm
  otutab_binary   Convert OTU table with counts to presence(1) / absence(0)
  otutab_forest_classify   Classify samples using random forest
  otutab_core   Identify core microbiome in OTU table
  otutab_forest_train  Train random forest classifier on OTU table
  otutab_otus   Extract OTU labels from OTU table
  otutab_rare  Sub-sample OTU table to same number of reads per sample
  otutab_samples  Extract sample labels from OTU table
  otutab_select   Identify OTUs which are informative (correlate with metadata)
  otutab_xtalk   Identify cross-talk using improved algorithm (UNCROSS2)
  search_pcr2   In-silico PCR, search for matches to primer pair
  subtree   Extracts subtree under given node
  tabbed2otutab   Convert read mapping file (read+OTU) to OTU table
  tree_subset   Extract subset of tree for given set of leaf labels