alpha_div_rare command
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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.



alpha_div_rare command

See also
  Abundance rarefaction
  Jagged steps in the fast rarefaction curve

The alpha_div_rare command calculates a rarefaction curve for an alpha diversity metric.

Note that this command currently does not currently account for discarding singletons. I doubt it matters in practice, because other sources of error are probably more important, so rarefaction analysis has dubious value for marker gene OTUs. If you are interested in a rarefaction command which accounts for singletons, please let me know and I will implement the feature.

Input is an OTU table in QIIME classic format.

The -metric option specifies a metric name. Default is richness. See alpha diversity metrics for supported metrics.

The specified metric is calculated by subsampling the OTU table at 1%, 2% ... 99%, 100% of the reads. The -method option specifies which subsampling method to use. Default is fast subsampling. See otutab_subsample command for discussion of subsampling and supported methods.

The output file is specified by the -output option. The output file is a tabbed text file with a header followed by 100 lines, one per subsample size. The first field is the subsample size as a percentage.

The output file can easily be loaded into a spreadsheet or other charting software for generating figures.


usearch -alpha_div_rare otutab.txt -output rare.txt