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SOCS is a mapping tool for SOLiD (color space) sequencing reads that supports bisulfite transformation for 5mC methylation studies. When run in bisulfite mode, alignments are tolerant of any number of bisulfite-induced nucleotide substitutions, allowing for unbiased alignment to standard reference sequences (without pre-conversion). See "Variant mode" in the Options section of the Usage document for more details.

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Publications

• Ondov BD, Cochran C, Landers M, Meredith GD, Dudas M, Bergman NH. An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System. Bioinformatics 2010 Aug 1;26(15):1901-2. Full text
• Ondov BD, Varadarajan A, Passalacqua KD, Bergman NH. Efficient mapping of ABI SOLiD sequence data to a reference genome for functional genomic applications. Bioinformatics 2008 Dec 1;24(23):2776-7. Full text