pick_closed_reference_otus.py – Closed-reference OTU picking/Shotgun UniFrac workflow.

Description:

This script picks OTUs using a closed reference 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: pick_closed_reference_otus.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: 2]

Output:

Pick OTUs, assign taxonomy, and create an OTU table against a reference set of OTUs. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).

pick_closed_reference_otus.py -i $PWD/seqs.fna -r $PWD/refseqs.fna -o $PWD/otus_w_tax/ -t $PWD/taxa.txt

Pick OTUs and create an OTU table against a reference set of OTUs without adding taxonomy assignments. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).

pick_closed_reference_otus.py -i $PWD/seqs.fna -r $PWD/refseqs.fna -o $PWD/otus/

Pick OTUs, assign taxonomy, and create an OTU table against a reference set of OTUs using usearch_ref. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).

pick_closed_reference_otus.py -i $PWD/seqs.fna -r $PWD/refseqs.fna -o $PWD/otus_usearch/ -p $PWD/usearch_params.txt -t $PWD/taxa.txt