pick_otus_through_otu_table.py – A workflow script for picking OTUs through building OTU tables

Description:

This script takes a sequence file and performs all processing steps through building the OTU table.

Usage: pick_otus_through_otu_table.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fp

The input fasta file [REQUIRED]

-o, --output_dir

The output directory [REQUIRED]

[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]

-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:

This script will produce an OTU mapping file (pick_otus.py), a representative set of sequences (FASTA file from pick_rep_set.py), a sequence alignment file (FASTA file from align_seqs.py), taxonomy assignment file (from assign_taxonomy.py), a filtered sequence alignment (from filter_alignment.py), a phylogenetic tree (Newick file from make_phylogeny.py) and an OTU table (from make_otu_table.py).

Simple example:

The following command will start an analysis on inseq1.fasta (-i), which is a post-split_libraries fasta file. The sequence identifiers in this file should be of the form <sample_id>_<unique_seq_id>. The following steps, corresponding to the preliminary data preparation, are applied.

1. Pick OTUs with uclust at similarity of 0.97;
2. Pick a representative set with the most_abundant method;
3. Align the representative set with PyNAST;
4. Assign taxonomy with RDP classifier;
5. Filter the alignment prior to tree building - remove positions which are all gaps, and specified as 0 in the lanemask;
6. Build a phylogenetic tree with FastTree;
7. Build an OTU table.

All output files will be written to the directory specified by -o, and subdirectories as appropriate.

pick_otus_through_otu_table.py -i inseqs1.fasta -o wf1/ -p custom_parameters.txt