1. Mark Howison
  2. gabi


gabi / README.md

GABI is developed by Mark Howison at the Center for Computation and Visualization, Brown University, in collaboration with Casey W. Dunn and Felipe Zapata of the Dunn Lab and Erika J. Edwards.

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:

export PREFIX=/usr/local

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:

gabi help

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