GS RunProcessor is the main part of the GS FLX Titanium system. The software is in charge of picture background normalization, signal location correction, cross-talk correction, signals conversion, and sequencing data generation. GS RunProcessor would produce a series of files including SFF (standard flowgram format) files each time after run. SFF files con­tain the basecalled sequences and corresponding quality scores for all indi­vidual, high-quality reads (filtered reads). And it could be viewed directly from the screen of GS FLX Titanium system. Using GS De Novo Assem­bler, GS Reference Mapper and GS Amplicon Variant Analyzer provided by GS FLX Titanium system, SFF files can be applied in multiaspects and converted into fastq format for further data analyzing.