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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 command

See also
  Alpha diversity
  alpha diversity metrics
  Recommended alpha and beta metrics
  Comparing alpha diversity between groups
  alpha_div_sig command
  beta_div command

The alpha_div command calculates one or more alpha diversity metrics for each sample in an OTU table. The OTU table must be in QIIME classic format.

To calculate the statistical significance of a change in metric between groups, use the alpha_div_sig command.

The -metrics option specifies one or more metric names separated by commas. Default is a few popular metrics. Popular does not necessarily mean recommended. See alpha diversity metrics for supported metrics.

Output is written to a table specified by the -output option. The file is in tabbed text format. Rows are samples, columns are metrics. This file can be loaded into spreadsheet software such as Excel for further analysis.

Example: calculate default metrics

usearch -alpha_div otutable.txt -output alpha.txt

Example: calculate Gini-Simpson index

usearch -alpha_div otutable.txt -output gini.txt -metrics gini_simpson

Example: calculate Chao1 and Berger-Parker indexes

usearch -alpha_div otutable.txt -output alpha.txt -metrics chao1,berger_parker