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[[http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration Quality Score Calibration Tool]] at the Broad Institute.
== Base Calling Tools ==
Erlich, Y., Mitra, P.P., delaBastide, M., McCombie, W.R., Hannon, G.J. (2008) Alta-Cyclic: A self-optimizing base caller for next-generation sequencing. ''Nature Methods'' '''5''':679-682
Kao, W.-C., Stevens, K., Song, Y.S. (2009) BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing. ''Genome Research'' '''19''':1884-1895
Whiteford, N., Skelly, T., Curtis, C., Ritchie, M.E., Löhr, A., Zaranek, A.W., Abnizova, I., Brown, C. (2009)
Swift: Primary data analysis for the Illumina Solexa sequencing platform. ''Bioinformatics'' '''25''':2194-2199
Rougemont, J., Amzallag, A., Iseli, C., Farinelli, L., Xenarios, I., Naef, F. (2008) Probabilistic base calling of Solexa sequencing data. ''BMC Bioinformatics'' '''9''':Article 431
