News and Announcements » – Compute shared OTUs between all pairs of samples


This script computes from an OTU table a matrix with the number of shared phylotypes between all pairs of samples.

Usage: [options]

Input Arguments:



-i, --otu_table_fp
Path to the input OTU table in biom format or a directory containing OTU tables
-o, --output_fp
The output filepath


-r, --reference_sample
Name of reference sample to which all pairs of samples should be compared [default: None]


Single example:

Compute shared OTUs on one OTU table for all samples -i otu_table.biom -o shared_otus.txt

Reference sample example:

Compute shared OTUs with respect to a reference sample. Computes shared OTUs between all pairs of samples and the reference sample. E.g. in a transplant study this can be used to establish a base line count of shared OTUs with the Donor sample before and after the transplant. -i otu_table.biom -o shared_otus_PC.636.txt -r PC.636

Batch mode example:

Compute shared OTUs for a set of OTU tables, e.g. from running, with an even number of sequences per sample. The resulting directory can be fed to, which computes mean, median and the standard deviation on the provided tables. -i rarefied_otu_tables/ -o shared_otus/