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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

otutab_freqs2counts command

See also
 
OTU commands
  OTU table
  Making an OTU table (otutab command)

Convert OTU table from frequencies to counts. The input file must be in QIIME classic format except that the table entries are floating point frequencies in the range 0 to 1.

The output file is specified by the -output option. It is written in QIIME classic format.

The desired total count for each sample is specified by the -sample_size option, default 10000.

A frequency is converted to a count using count = frequency * sample_size and rounding to the nearest integer. The total after conversion may be slightly different from sample_size due to rounding.

Example

usearch -otutab_freqs2counts otutable_freqs.txt -output otutable_counts.txt