Allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots. Rolexa is based on a base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. It provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. This method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%.