SOCS uses iterative mismatch tolerances to speed up high tolerance mapping. It finds optimal alignments for each read across one or more reference files. Maps of sequence census and valid sequence-space mismatches are also provided. For repeated reference regions, all matches are recorded and their sequence census is kept separately.
Source and MacOSX executable available in the “Files” section.
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For more information and sample data, see socs.biology.gatech.edu.