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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.



ublast command

Sensitive database search using the UBLAST algorithm. Alignments are local.

An E-value threshold must be specified.

A database file must be specified using the -db option. FASTA and .udb formats are supported. For large databases, .udb format is recommended (see makeudb_ublast command).

The -strand option is required for nucleotide databases.

Nucleotide, protein and translated searches are supported.

The -accel option tunes search speed against sensitivity. Smaller values are faster but tend to have lower sensitivity to hits with lower sequence identity. Default is 0.8. See UBLAST algorithm for more discussion.

See also
  Output files
Accept options
  Weak hits (Weak hits are especially useful with ublast)
  Termination options
  Indexing options
  Masking options
  Alignment parameters
  Alignment heuristics


usearch -ublast reads.fasta -db proteins.udb -evalue 1e-9 -accel 0.5 -alnout results.aln