alpha_div 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 command

See also
alpha diversity metrics
  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.

The -metrics option specifies one or more metric names separated by commas. Default is all metrics. 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 all 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