News and Announcements » – A workflow for running a core set of QIIME diversity analyses.


This script plugs several QIIME diversity analyses together to form a basic workflow beginning with a BIOM table, mapping file, and optional phylogenetic tree.

The included scripts are those run by the workflow scripts,,, plus the (non-workflow) scripts,, and To update parameters to the workflow scripts, you should pass the same parameters file that you would pass if calling the workflow script directly.

Additionally, a table summary is generated by running the ‘biom summarize-table’ command (part of the biom-format package). To update parameters to this command, your parameters file should use ‘biom-summarize-table’ (without quotes) as the script name. See for more details.

Usage: [options]

Input Arguments:



-i, --input_biom_fp
The input biom file [REQUIRED]
-o, --output_dir
The output directory [REQUIRED]
-m, --mapping_fp
The mapping filepath [REQUIRED]
-e, --sampling_depth
Sequencing depth to use for even sub-sampling and maximum rarefaction depth. You should review the output of the ‘biom summarize-table’ command to decide on this value.


-p, --parameter_fp
Path to the parameter file, which specifies changes to the default behavior. For more information, see [if omitted, default values will be used]
-a, --parallel
Run in parallel where available. Specify number of jobs to start with -O or in the parameters file. [default: False]
Apply non-phylogenetic alpha (chao1 and observed_otus) and beta (bray_curtis) diversity calculations. This is useful if, for example, you are working with non-amplicon BIOM tables, or if a reliable tree is not available (e.g., if you’re working with ITS amplicons) [default: False]
Suppress generation of taxa summary plots. [default: False]
Suppress beta diversity analyses. [default: False]
Suppress alpha diversity analyses. [default: False]
Suppress OTU/category significance analysis. [default: False]
-t, --tree_fp
Path to the tree file if one should be used. Required unless –nonphylogenetic_diversity is passed. [default: no tree will be used]
-c, --categories
The metadata category or categories to compare (i.e., column headers in the mapping file) for categorical analyses. These should be passed as a comma-separated list. [default: None; do not perform categorical analyses]
-w, --print_only
Print the commands but don’t call them – useful for debugging or recovering from failed runs. [default: False]
Don’t fail if output directory exists, but attempt to recover from the failed run. [default: False]
-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]


Run diversity analyses at 20 sequences/sample, with categorical analyses focusing on the SampleType and day categories. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/). -i $PWD/otu_table.biom -o $PWD/core_output -m $PWD/map.txt -c SampleType,day -t $PWD/rep_set.tre -e 20