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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.



Sequence database search

  makeudb_sintax  Make UDB database file for sintax
  makeudb_ublast  Make UDB database file for ublast
  makeudb_usearch  Make UDB database file for usearch_global
  search_exact  Search for identical sequences
  search_global  Search database using global alignment without speed heuristics
  search_local  Search database using locbal alignment without speed heuristics
  search_oligodb  Search for matches to short nucleotide sequences, e.g. primers
  search_pcr  In-silico PCR, search for matches to pairs of primers in database
  search_pcr2  In-silico PCR, search for matches to primer pair
  search_peptidedb  Search for matches to short peptide sequences
  search_phix  Search for matches to PhiX sequence
  ublast  Fast database search using local alignment (much faster than BLAST)
  usearch_global  Fast database search using global alignment
  usearch_local  Fast database search using local alignment