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.. _pick_reference_otus_through_otu_table:
.. index:: pick_reference_otus_through_otu_table.py
*pick_reference_otus_through_otu_table.py* -- Reference OTU picking/Shotgun UniFrac workflow.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script picks OTUs using a reference-based method and constructs an OTU table. Taxonomy is assigned using a pre-defined taxonomy map of reference sequence OTU to taxonomy. If full-length genomes are provided as the reference sequences, this script applies the Shotgun UniFrac method.
**Usage:** :file:`pick_reference_otus_through_otu_table.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_fp
The input sequences
-r, `-`-reference_fp
The reference sequences
-o, `-`-output_dir
The output directory
**[OPTIONAL]**
-p, `-`-parameter_fp
Path to the parameter file, which specifies changes to the default behavior. See http://www.qiime.org/documentation/file_formats.html#qiime-parameters . [if omitted, default values will be used]
-t, `-`-taxonomy_fp
The taxonomy map [default: None]
-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]
-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:**
Pick OTUs, assign taxonomy, and create an OTU table against a reference set of OTUs.
::
pick_reference_otus_through_otu_table.py -i inseqs.fasta -r refseqs.fasta -o out -p qiime_parameters.txt -t taxa.txt
Pick OTUs and create an OTU table against a reference set of OTUs without adding taxonomy assignments.
::
pick_reference_otus_through_otu_table.py -i inseqs.fasta -r refseqs.fasta -o out -p qiime_parameters.txt
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