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

Brian D. Ondov, Anjana Varadarajan, Karla D. Passalacqua, Nicholas H. Bergman
2008 Computer applications in the biosciences : CABIOS  
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.
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doi:10.1093/bioinformatics/btn512 pmid:18842598 pmcid:PMC2639273 fatcat:5d46ygbowvafhlaxdcrxw73y7y