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The script tabulates the number of times an OTU is found in each sample, and adds the taxonomic predictions for each OTU in the last column if a taxonomy file is supplied.

Usage: [options]

Input Arguments:



-i, --otu_map_fp
Path to the input OTU map (i.e., the output from
-o, --output_biom_fp
The output otu table in biom format (recommended extension: .biom)


-t, --taxonomy
Path to taxonomy assignment, containing the assignments of taxons to sequences (i.e., resulting txt file from [default: None]
-e, --exclude_otus_fp
Path to a file listing OTU identifiers that should not be included in the OTU table (e.g., the output of or a fasta file where seq ids should be excluded (e.g., failures fasta file from


The output of is a biom file, where the columns correspond to Samples and rows correspond to OTUs and the number of times a sample appears in a particular OTU.

Make OTU table:

Make an OTU table from an OTU map (i.e., result from and a taxonomy assignment file (i.e., result from Write the output file to otu_table.biom. -i otu_map.txt -t tax_assignments.txt -o otu_table.biom

Make OTU table, excluding OTU ids listed in a fasta file:

Make an OTU table, excluding the sequences listed in pynast_failures.fna. Note that the file pass as -e must end with either ‘.fasta’ or ‘.fna’. -i otu_map.txt -o otu_table_no_pynast_failures.biom -e pynast_failures.fna

Make OTU table, excluding a list of OTU ids:

Make an OTU table, excluding the sequences listed in chimeric_seqs.txt -i otu_map.txt -o otu_table_non_chimeric.biom -e chimeric_seqs.txt

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