News and Announcements » – A workflow for de novo OTU picking, taxonomy assignment, phylogenetic tree construction, and OTU table construction.


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

Usage: [options]

Input Arguments:



-i, --input_fp
The input fasta file [REQUIRED]
-o, --output_dir
The output directory [REQUIRED]


-p, --parameter_fp
Path to the parameter file, which specifies changes to the default behavior. See . [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: 2]


This script will produce an OTU mapping file (, a representative set of sequences (FASTA file from, a sequence alignment file (FASTA file from, taxonomy assignment file (from, a filtered sequence alignment (from, a phylogenetic tree (Newick file from and a biom-formatted OTU table (from

Simple example:

The following command will start an analysis on seqs.fna (-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: Pick de novo OTUs at 97%; pick a representative sequence for each OTU (the OTU centroid sequence); align the representative set with PyNAST; assign taxonomy with the uclust consensus taxonomy assigner; filter the alignment prior to tree building - remove positions which are all gaps, and specified as 0 in the lanemask; build a phylogenetic tree with FastTree; build an OTU table. All output files will be written to the directory specified by -o, and subdirectories as appropriate. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/). -i $PWD/seqs.fna -o $PWD/otus/

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