A repository for storing code and data related to a systematic comparison of short read taxonomy assignment tools. Includes a framework to facilitate the evaluation and comparison of additional taxonomy assigners in the context of the results presented in (Bokulich, Rideout, et al. (Nature Methods, under review)).
To run the code in this repository, you will need the development version of
QIIME (tested on 1.7.0-dev, master@dc1ca5e) and
IPython >= 1.0.0 installed, with
short-read-tax-assignment/code added to your PYTHONPATH and
short-read-tax-assignment/code/scripts added to your PATH.
To test your installation/setup, you can run the unit tests with the following
commands (assuming you are in the short-read-tax-assignment directory and
you have nose installed):
nosetests code
To view and interact with an IPython Notebook, change into the directory containing the IPython Notebooks of interest, and start an IPython Notebook server. For example:
cd short-read-tax-assignment/demo/eval-demo
ipython notebook
This will launch a web browser. You can then open the notebook by clicking on its name, and execute the notebook.
Two IPython Notebooks are provided to illustrate how to run a parameter sweep on a concept design for a new taxonomic assigner, and then evaluate that in the context of pre-computed results (the evaluation data from this study). The notebooks can be found under short-read-tax-assignment/demo/eval-demo
Requirements for running the usearch example parameter sweep notebook, in addition to the code in this repository:
- Python 2.7
- IPython Notebook
- usearch v5.2.236.
- pyqi 0.2.0
- biom-format 1.2.0
- uc_to_assignments (A gist written for use in this notebook)
Requirements for running the evaluation framework notebook, in addition to the code in this repository:
- Python 2.7
- IPython Notebook
- QIIME
- PyCogent
- matplotlib