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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.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11

clusters option

Specifies a filename prefix for saving clusters. Supported by cluster_fast only. The sequences in each cluster are written to a separate FASTA file. The first sequence in the file is always the centroid. The filename is constructed by appending an integer cluster number 0, 1, 2... to the string specified by -clusters.

The value of -clusters may include a path, which must exist. In the example below, the cluster filenames will be cluster_dir/c_0, cluster_dir/c_1 etc.

Example

usearch -cluster_fast seqs.fa -id 0.90 -clusters cluster_dir/c_