Overview

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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:

http://ccv.brown.edu/mhowison/gabi-report

Installation

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:

export PREFIX=$HOME

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.

Issues

If you find a bug or encounter a problem running GABI, please submit it through
the Bitbucket issue tracker.

Citing

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

License

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