Distribution-based OTU calling

dbotu3 is a new implementation of Sarah Preheim''s dbOTU algorithm. The scope is narrower, the numerical comparisons are faster, and the interface is more user-friendly.

Read the documentation for:

• a guide to getting started,
• an explanation of the algorithm, and
• the API reference.

You can also read our new paper for more technical details about the algorithm.

The Alm Lab website also has a short page with information.

For more information on installation, version histories, and how to contribute, please go to the project's repo.

Installation

dbotu3 is on conda and can be installed as follows:

conda install -c cduvallet -c conda-forge dbotu

Note: the anaconda.org installation instruction (which is missing the -c conda-forge part) won't work because conda won't know where to find the python-levenshtein package.

For QIIME 2 users, dbotu3 is also available as a plugin.

The PyPi package is no longer updated.

Requirements

• Numpy, SciPy, BioPython, Pandas
• Levenshtein

Version history

• 1.5.3: update README to update description on anaconda.org
• 1.5.2: re-organize files so that package is more canonical and plays well with conda
• 1.1 - 1.5: ??
• 1.1: Corrected error where sequence IDs that could be read as integers would not be found in the table
• 1.2: Python 2 compatibility, tox test framework, warnings for improperly-formatted sequence count tables
• 1.2.1: Added setup requirements
• 1.3.0: Improved OTU file header. Split the log file into a debug and progress log.
• 1.4.0: Made an improvement to the Levenshtein-based genetic dissimilarity metric.
• 1.4.1: Account for pandas API change to MultiIndex
• 1.5.0: Added the restart and rep seq scripts
• 1.5.1: New function for Qiime2 compatibility
• 1.5.2: Move files around to make this a Python package (rather than dbotu.py script)
• 1.5.3: Point to conda, rather than PyPi, installation

To-do

• Testing for the restart scripts
• Better coverage for unit tests

Building the package

dbotu3 was originally made as a pip package. However, after writing the dbotu QIIME 2 plugin, it was switched to conda. The pip package is no longer updated.

To re-build an updated version of the dbotu package:

conda-build recipe/ -c conda-forge

This builds a local version of the package (specified in meta.yaml, source: path: ../). The contents of the dbotu package content are specified in dbotu/__init__.py. The scripts in scripts/ are accessories, and aren't actually used by the package/module.

Citation

If you use dbOTU3 in a scientific paper, we ask that you cite the original dbOTU publication (Preheim et al.) or the dbOTU3 publication:

Preheim et al. Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit. Appl Environ Microbiol (2013) doi:10.1128/AEM.00342-13.

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.

Author

If you find a bug or have a request for a new feature, open an issue_.

.. _issue: https://github.com/almlab/dbotu3/issues

Scott Olesen / swo at alum.mit.edu