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MGTAXA

A free software for taxonomic classification of metagenomic sequences with machine learning techniques

This project aims to develop a toolbox for reliable assignment of species composition to large collections of unassembled environmental sequencing data, with automated and regular updates of databases and models. The software combines a Web server front-end with a high-performance computational back-end to let a wide community of biologists build classification models specific to their metagenomic samples.

A free public computational Web server for metagenomic taxonomic assignment is available at http://mgtaxa.jcvi.org. The server makes predictions for all domains of life as well as viruses. It also predicts probable hosts for the bacteriophage sequences.

Dependencies

Python, Numpy, Shogun, MySQL, HDF5, PyTables

Install

Install the dependencies
Edit the Makefile and define the necessary environment variables
from the top directory, do:
mkdir build && cd build
make -f ../Makefile
make install

Documentation

Auto-generated API documentation

Sub-projects

License

GPLv3

Authors

Andrey Tovchigrechko (atovtchi@jcvi.org)
Seung-Jin Sul (ssul@jcvi.org)

Contact

Andrey Tovchigrechko (atovtchi@jcvi.org)

Support

Find or submit an issue

Read or edit wiki

Funding

This software is developed at J. Craig Venter Institute with the financial support from the U.S. National Science Foundation grant 0850256 and the U.S. Department of Energy grant DE-FC02-02ER63453.

Download

You can download this project in either zip or tar formats.

You can also clone the project with Git by running:

$ git clone git://github.com/andreyto/mgtaxa