An efficient basecaller for Illumina sequencers with calibrated quality scores. freeIbis offers significant improvements in sequence accuracy owing to the use of a novel multiclass support vector machine (SVM) algorithm. This approach produces more accurate basecalls than the default Illumina basecaller. freeIbis can use the control sequences to calibrate the output of the SVM to produce directly calibrated quality scores. For instance, freeIbis can produce quality scores that correlate highly with observed ones.