News and Announcements » – A workflow script for performing alpha rarefaction


The steps performed by this script are: Generate rarefied OTU tables; compute alpha diversity metrics for each rarefied OTU table; collate alpha diversity results; and generate alpha rarefaction plots.

Usage: [options]

Input Arguments:



-i, --otu_table_fp
The input otu table [REQUIRED]
-m, --mapping_fp
Path to the mapping file [REQUIRED]
-o, --output_dir
The output directory [REQUIRED]


-p, --parameter_fp
Path to the parameter file, which specifies changes to the default behavior. See . [if omitted, default values will be used]
-n, --num_steps
Number of steps (or rarefied OTU table sizes) to make between min and max counts [default: 10]
-f, --force
Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: None]
-w, --print_only
Print the commands but don’t call them – useful for debugging [default: False]
-a, --parallel
Run in parallel where available [default: False]
-t, --tree_fp
Path to the tree file [default: None; REQUIRED for phylogenetic measures]
The lower limit of rarefaction depths [default: 10]
-e, --max_rare_depth
The upper limit of rarefaction depths [default: median sequence/sample count]
-O, --jobs_to_start
Number of jobs to start. NOTE: you must also pass -a to run in parallel, this defines the number of jobs to be started if and only if -a is passed [default: 1]
Retain intermediate files: rarefied OTU tables (rarefaction) and alpha diversity results (alpha_div). By default these will be erased [default: False]


The primary interface for the results will be OUTPUT_DIR/alpha_rarefaction_plots/rarefaction_plots.html where OUTPUT_DIR is the value you specify with -o. You can open this in a web browser for interactive alpha rarefaction plots.


Given an OTU table, a phylogenetic tree, a mapping file, and a max sample depth, compute alpha rarefaction plots for the PD, observed species and chao1 metrics. To specify alternative metrics pass a parameter file via -p. We generally recommend that the max depth specified here (-e) is the same as the even sampling depth provided to beta_diversity_through_plots (also -e). -i otu_table.biom -o arare_max100/ -t rep_set.tre -m Fasting_Map.txt -e 100