Methods and apparatuses for estimating parameters in a predictive model for use in sequencing-by-synthesis

A method of sequencing a sample nucleic acid template, comprising:

• (a) measuring signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto an array of wells including (i) a first well containing the sample nucleic acid template and (ii) a plurality of other sample-containing wells, wherein the array includes a sensor array for detecting the signal data related to the chemical reactions resulting from the flow of nucleotides, wherein the signal data are received from the sensor array;
• (b) determining preliminary sequence information for the sample nucleic acid template using the signal data from the first well;
• (c) constructing a phase-state model for a first set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter fitted by comparing signal data from the plurality of other sample-containing wells to predicted signals for the plurality of other sample-containing wells resulting from the first set of nucleotide flows, and wherein the model is stored in a machine-readable memory;
• and
• (d) determining revised sequence information for the sample nucleic acid template by performing a base calling analysis of the signal data from the first well using the signal correction parameter fitted based on signal data from the plurality of other sample-containing wells,
• wherein the first well containing the sample nucleic acid template is part of a first set of wells in a first region of the array, the plurality of other sample-containing wells are part of a second set of wells in the first region of the array, and the first set of wells and the second set of wells are distinguishable from one another within the first region of the array by shape, dimension, or inclusion in a defined spatial arrangement that is an alternating arrangement wherein positions of the wells of the first set of wells alternate with positions of the wells of the second set of wells, and
• wherein the array further includes additional regions of the array that have additional respective first and second sets of wells that are distinguishable from one another within each of the additional regions of the array.