A method includes exposing template polynucleotide strands, sequencing primers, and polymerase to flows of nucleotide species; obtaining a series of measured intensity values and randomly selecting a training subset therefrom; generating series of base calls using a base caller and aligning the series of base calls to a reference genome or sequence using an aligner; determining intensity value thresholds and parameters of a linear transformation corresponding to different homopolymer lengths and nucleotide species; generating series of base calls corresponding to the series of measured intensity values using at least some of the parameters of a linear transformation; and recalibrating the series of base calls corresponding to the plurality of series of measured intensity values using at least some of the intensity value thresholds.