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Bioinformatics Advance Access published online on October 7, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn512
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications

Brian Ondov 1, Anjana Varadarajan 1, Karla D. Passalacqua 1 and Nicholas H. Bergman 1,2,*

1School of Biology, Georgia Institute of Technology, 310 Ferst Dr., Atlanta, GA 30332-0230
2Electro-Optical Systems Laboratory, Georgia Tech Research Institute, 925 Dalney St., Atlanta, GA 30332-0810

*To whom correspondence should be addressed. Prof. Nicholas H. Bergman, E-mail: nickbergman{at}gatech.edu


  Abstract

Summary: Here we report the development of SOCS (Short Oligonucleotide Color Space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of ‘color space’, and it maximizes usable data by allowing a user-specified number of mismatches. Sequence census functions facilitate a variety of functional genomics applications, including transcriptome mapping and profiling, as well as ChIP-Seq.

Availability: Executables, source code, and sample data are available at http://socs.biology.gatech.edu/

Contact: nickbergman{at}gatech.edu

Supplementary information: Available at Bioinformatics online.

Associate Editor: Prof. John Quackenbush

Received on May 2, 2008; revised on September 26, 2008; accepted on October 1, 2008

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