Distribution-based OTU calling

This software, dbOTU3, is the third major implementation of the distribution-based OTU-calling algorithm formulated by Preheim et al. [1], an extremely accurate algorithm for grouping DNA sequences from microbial communities into OTUs for ecological or biomedical research.

Unlike most OTU-calling approaches, which group sequences based only on the similarities of the sequences themselves, this algorithm also uses information about the distribution of sequences across samples. This allows dbOTU to distinguish ecologically-distinct but sequence-similar organisms or populations.

This documentation includes a guide to getting started, description of the algorithm, a comparison of the methodologies of the different implementations, and an API reference. The technical details of this implementation are also included in a publication [2] (although note the Caveat about the publication’s genetic criterion).

Indices and tables

[1]Preheim et al. Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit. Appl Environ Microbiol (2013) doi:10.1128/AEM.00342-13.
[2]Olesen SW, Duvallet C, and Alm EJ. dbOTU3: A new implementation of distribution-based OTU calling. PLoS ONE (2017) doi:10.1371/journal.pone.0176335.