Extracting barcode split data from SOLiD 5500 XSQ files can be done by using ABI XSQ_Tools, currently installed at /home/daras/XSQ_Tools.
1. To split the XSQ files into multiple XSQ files, by barcode:
convertFromXSQ.sh -s xsqfile -o outputpath
2. To convert each of the resulting XSQ files into csfasta and QV files:
convertFromXSQ.sh -c xsqfile
The converted files are created in the following directory: ./Libraries/<LibraryName>/<TagName>/reads
Typing just the command by itself will display all possible command line options and parameters.