Overview of GABI
Genome Assembly by Bayesian Inference (GABI) is a prototype of a Bayesian framework for sequence assembly.
An example report showing an assembly of the PhiX174 phage is available at:
GABI is experimental software and is not ready for production use. To test it, you will need to first install:
These instructions assume you are installing to a directory
$PREFIX, such as:
Alternatively, you might use your home directory as the prefix:
To install GABI, run:
./configure --prefix=$PREFIX make install
To run GABI, make sure that
$PREFIX/bin is in your path, and try:
See the phix-test directory for instructions and sample data for testing GABI on the PhiX174 genome.
If you find a bug or encounter a problem running GABI, please submit it through the Bitbucket issue tracker.
We have a preprint describing GABI available on arXiv:
Howison M, Zapata F, Edwards EJ, Dunn CW. (2013) Bayesian genome assembly and assessment by Markov Chain Monte Carlo sampling. arXiv:1308.1388
Copyright 2013-2014, Brown University, Providence, RI. All Rights Reserved.
GABI is distributed under the GNU General Public License version 3. For more information, see LICENSE or visit: http://www.gnu.org/licenses/gpl.html