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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.



Command categories

  Sequence alignment commands
  Chimera detection and filtering
  Sequence, tree and graph-based clustering
  Distance matrices
  Commands for diversity analysis
  Commands for reads in FASTQ format
  Commands for sequences in FASTx format (FASTA and FASTQ)
  Machine learning and finding informative OTUs
  Miscellaneous commands
  Commands for OTU analysis and denoising
  OTU table commands
  Next-generation reads
  Sequence database search
  Taxonomy commands
  Tree commands
  Labels and annotations