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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

beta_div command

See also
 
Diversity analysis
 
Beta diversity
 
beta diversity metrics
  alpha_div command

The beta_div command calculates one or more beta diversity metrics from 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 supported metric names. See beta diversity metrics for supported names.

For each metric, up to three output files are generated: a distance matrix in square format, a sorted distance matrix and a tree.

Trees are written in Newick format.

Sorted matrices and trees are generated only for metrics which support clustering; see beta diversity metrics. In a sorted distance matrix, samples are sorted to bring similar samples together.

Output file names are based on the metric name. The -filename_prefix option species a string to be added at the beginning of all output filenames. Typically this is a directory name, which must end with a slash or backslash. The directory must exist; usearch will not create a new directory. Default is no prefix.

The -mx_suffix, -sorted_mx_suffix and -tree_suffix options specify strings to be added at the end of the output filenames. Default values are .txt, .sorted.txt and .tree, respectively.

The Unifrac metric requires a tree for the OTUs, which is specified using the -tree option. The file must be in Newick format. The tree can be generated using the -cluster_agg command using the OTU FASTA file as input. If no tree is specified, the Unifrac metric will not be calcualated.

Example: calculate all supported beta metrics and write results in current directory

usearch -beta_div otutable.txt

Example: calculate all supported beta metrics and write output in directory /results/beta

usearch -beta_div otutable.txt -filename_prefix /results/beta/

Example: calculate Jaccard only and write results in current directory

usearch -beta_div otutable.txt -metrics jaccard
 
Example: calculate Jaccard and Bray-Curtis and write results in current directory

usearch -beta_div otutable.txt -metrics jaccard,bray_curtis