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

UNLABELLED 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/