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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.


 New in v11 

otutab_rare command

Subsamples ("rarefies") an OTU table to a fixed number of reads per sample using random subsampling without replacement. I now believe this is the best strategy because preserves the shape of the abundance distribution in each sample more accurately than systematic rounding as used in the obsolete otutab_norm command.

I recommend using this command to normalize samples to the same number of reads so that they are comparable to each other.

The output filename is specified by the output option.

Input and output are in QIIME classic format.

The number of reads per sample is specified by the -sample_size option. This option must be specified; there is no default value.

Samples which have < sample_size reads are discarded.

The -randseed option specifies a random number seed. The value must be a non-negative integer. By default, the seed is randomized using the operating system clock and process id so it will be different each time the command is executed. This option can be used to get reproducible results, e.g. -randseed 1.


usearch -otutab_rare otutab.txt -sample_size 5000 -output otutab_5k.txt