make_otu_table.py – Make OTU table

Description:

The script make_otu_table.py 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: make_otu_table.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_map_fp

Path to the input OTU map (i.e., the output from pick_otus.py)

-o, --output_biom_fp

The output otu table in biom format (recommended extension: .biom)

[OPTIONAL]

-t, --taxonomy

Path to taxonomy assignment, containing the assignments of taxons to sequences (i.e., resulting txt file from assign_taxonomy.py) [default: None]

-m, --mapping_fp

The mapping filepath

-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 identify_chimeric_seqs.py) or a fasta file where seq ids should be excluded (e.g., failures fasta file from align_seqs.py)

Output:

The output of make_otu_table.py 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 pick_otus.py) and a taxonomy assignment file (i.e., result from assign_taxonomy.py). Write the output file to otu_table.biom.

make_otu_table.py -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’.

make_otu_table.py -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

make_otu_table.py -i otu_map.txt -o otu_table_non_chimeric.biom -e chimeric_seqs.txt

Make OTU table, passing a mapping file with sample metadata:

Make an OTU table from an OTU map (i.e., result from pick_otus.py). Write the output file to otu_table.biom.

make_otu_table.py -i otu_map.txt -t tax_assignments.txt -o otu_table.biom -m mapping_file.txt