short-read-tax-assignment's Introduction

short-read-tax-assignment

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)).

Installing

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.

Testing your installation

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

Using the IPython Notebooks included in this repository

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.

Evaluation workflows, for testing new taxonomic assignment methods

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:

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