Bioinformatics. 2008 Oct 7. [Epub ahead of print]
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.
Ondov B, Varadarajan A, Passalacqua KD, Bergman NH.
School of Biology, Georgia Institute of Technology, 310 Ferst Dr., Atlanta, GA 30332-0230.
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.
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