Distribution-based OTU calling
Python Makefile
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
data
doc
pyenvironment
scripts
test
.gitignore
Makefile
README.rst
__init__.py
dbotu.py
requirements.readthedocs.txt
requirements.txt
setup.py
tox.ini

README.rst

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.

Installation

dbotu3 is on PyPi and can be installed with pip:

pip install dbotu

dbotu3 is also on conda and can be installed as follows:

conda install -c cduvallet -c conda-forge dbotu

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

Requirements

Version history

  • 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

To-do

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

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.

Scott Olesen / swo at alum.mit.edu