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.
Python, Numpy, Shogun, MySQL, HDF5, PyTables
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
Auto-generated API documentation
GPLv3
Andrey Tovchigrechko (atovtchi@jcvi.org)
Seung-Jin Sul (ssul@jcvi.org)
Andrey Tovchigrechko (atovtchi@jcvi.org)
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.
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