core_diversity_analyses.py – A workflow for running a core set of QIIME diversity analyses.

Description:

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 alpha_rarefaction.py, beta_diversity_through_plots.py, summarize_taxa_through_plots.py, plus the (non-workflow) scripts make_distance_boxplots.py, compare_alpha_diversity.py, and group_significance.py. 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 http://qiime.org/documentation/qiime_parameters_files.html for more details.

Usage: core_diversity_analyses.py [options]

Input Arguments:

Note

[REQUIRED]

-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.

[OPTIONAL]

-p, --parameter_fp

Path to the parameter file, which specifies changes to the default behavior. For more information, see www.qiime.org/documentation/qiime_parameters_files.html [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]

--nonphylogenetic_diversity

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_taxa_summary

Suppress generation of taxa summary plots. [default: False]

--suppress_beta_diversity

Suppress beta diversity analyses. [default: False]

--suppress_alpha_diversity

Suppress alpha diversity analyses. [default: False]

--suppress_group_significance

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]

--recover_from_failure

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]

Output:

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/).

core_diversity_analyses.py -i $PWD/otu_table.biom -o $PWD/core_output -m $PWD/map.txt -c SampleType,day -t $PWD/rep_set.tre -e 20