dbotu 1.2

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 manuscript 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.

Requirements

• Numpy, SciPy, BioPython, Pandas

• Levenshtein

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

To-do

• Better coverage for unit tests

Author

Scott Olesen / swo at alum.mit.edu