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Distribution-based OTU calling

Project description

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 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.

The PyPi package is no longer update.

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
  • 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

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

Project details


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