alpha_diversity.py – Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics

Description:

This script calculates alpha diversity, or within-sample diversity, using an OTU table. The QIIME pipeline allows users to conveniently calculate more than two dozen different diversity metrics. The full list of available metrics is available by passing the -s option to this script.

Documentation of the metrics can be found at http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html. Every metric has different strengths and limitations - technical discussion of each metric is readily available online and in ecology textbooks, but is beyond the scope of this document.

Usage: alpha_diversity.py [options]

Input Arguments:

Note

[OPTIONAL]

-i, --input_path

Input OTU table filepath or input directory containing OTU tables for batch processing. [default: None]

-o, --output_path

Output filepath to store alpha diversity metric(s) for each sample in a tab-separated format or output directory when batch processing. [default: None]

-m, --metrics

Alpha-diversity metric(s) to use. A comma-separated list should be provided when multiple metrics are specified. [default: PD_whole_tree,chao1,observed_otus]

-s, --show_metrics

Show the available alpha-diversity metrics and exit.

-t, --tree_path

Input newick tree filepath. [default: None; REQUIRED for phylogenetic metrics]

Output:

The resulting file(s) is a tab-delimited text file, where the columns correspond to alpha diversity metrics and the rows correspond to samples and their calculated diversity measurements. When a folder is given as input (-i), the script processes every otu table file in the given folder, and creates a corresponding file in the output directory.

Example Output:

	simpson	PD_whole_tree	observed_otus
PC.354	0.925	2.83739	16.0
PC.355	0.915	3.06609	14.0
PC.356	0.945	3.10489	19.0
PC.481	0.945	3.65695	19.0
PC.593	0.91	3.3776	15.0
PC.607	0.92	4.13397	16.0
PC.634	0.9	3.71369	14.0
PC.635	0.94	4.20239	18.0
PC.636	0.925	3.78882	16.0

Single File Alpha Diversity Example (non-phylogenetic):

To perform alpha diversity (e.g. chao1) on a single OTU table, where the results are output to “alpha_div.txt”, you can use the following command:

alpha_diversity.py -i otu_table.biom -m chao1 -o adiv_chao1.txt

Single File Alpha Diversity Example (phylogenetic):

In the case that you would like to perform alpha diversity using a phylogenetic metric (e.g. PD_whole_tree), you can use the following command:

alpha_diversity.py -i otu_table.biom -m PD_whole_tree -o adiv_pd.txt -t rep_set.tre

Single File Alpha Diversity Example with multiple metrics:

You can use the following idiom to run multiple metrics at once (comma-separated):

alpha_diversity.py -i otu_table.biom -m chao1,PD_whole_tree -o adiv_chao1_pd.txt -t rep_set.tre

Multiple File (batch) Alpha Diversity:

To perform alpha diversity on multiple OTU tables (e.g.: rarefied otu tables resulting from multiple_rarefactions.py), specify an input directory instead of a single otu table, and an output directory (e.g. “alpha_div_chao1_PD/”) as shown by the following command:

alpha_diversity.py -i otu_tables/ -m chao1,PD_whole_tree -o adiv_chao1_pd/ -t rep_set.tre