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ABBA: Assembly Boosted By Amino acid sequences |
Overview
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. See the journal paper.
For additional information on short read assembly check the following University of Maryland CBCB web sites:
System requirements
ABBA consists of a collection of C/C++ and Perl modules running under Unix. The Perl components rely on Perl 5.6.0 or later. You can obtain a current version of Perl from CPAN if one is not already installed on your system. The C/C++ components have been tested under gcc 2.9x and 3.x on Linux RedHat 7.3, Mac OSX, and OSF1 V5.1. We expect the code will compile with minimal changes on any other Unix-based operating system.
Obtaining ABBA
This software is OSI
Certified Open Source Software.
Documentation
Compiling minimus involves the following steps:
- Unpack the AMOS distribution:
gzip -dc amos-<version>.tar.gz | tar -xf -
(replace <version> with the current version of the distribution. - Change directories to the top level of the distribution:
cd amos-<version> - Run the configuration script that identifies the specific configuration
of your system.
./configure --disable-all --enable-ABBA
At this step you may also specify the location where you want the code to be ultimately installed:
./configure --disable-all --enable-ABBA --prefix=/usr/local/
By default the code will be installed in the directory from which you ran theconfigurecommand - Compile the code
make all - Install the binaries in the appropriate locations
make install
Documentation on running ABBA is included with the distribution in
the /docs subdirectory.
Contact Information
You can contact us at:
References
Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads. Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186