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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.



sortbysize command

See also
Abundance sort
  UCLUST sort order
  Global trimming

Sort sequences by decreasing size annotation, which usually refers to the size of a cluster. The size is specified by a field size=N; in the sequence label, where N is an integer. The -minsize and -maxsize options can be used to specify a minimum and maximum size, respectively.

Output is written to a FASTA file using the -fastaout option and/or a FASTQ file using the -fastqout option.

For most applications, it is recommended that sequences are globally trimmed before clustering and abundance sorting.

The -relabel prefix option can be used to generate sequential labels for the sorted sequences. The output label is prefixN where N=1, 2, 3 etc. If -sizeout is used, a size annotation will be appended to the sequential label.

The -topn N option specifies that no more than N sequences should be output.


usearch -sortbysize seqs.fasta -fastaout seqs_sorted.fasta -minsize 4