Journal Article

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

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

in Bioinformatics

Volume 24, issue 23, pages 2776-2777
Published in print December 2008 | ISSN: 1367-4803
Published online October 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn512

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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@gatech.edu

Supplementary information: Supplementary data are available at Bioinformatics Online.

Journal Article.  1641 words. 

Subjects: Bioinformatics and Computational Biology

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