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.
dbotu3 is also on conda and can be installed as follows:
conda install -c cduvallet -c conda-forge dbotu
The PyPi package is no longer update.
- 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
- Testing for the restart scripts
- Better coverage for unit tests
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.
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size||File type||Python version||Upload date||Hashes|
|Filename, size dbotu-1.5.3-py3-none-any.whl (11.5 kB)||File type Wheel||Python version py3||Upload date||Hashes View|