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

1. A method of estimating a parameter related to sequencing of a sample nucleic acid template, comprising:

(a) measuring signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto a sensor array comprising a plurality of regions of wells, at least one of the regions of wells comprising: (i) a first set of wells including a first well containing the sample nucleic acid template and (ii) a second set of wells including a plurality of other sample-containing wells, wherein the first set of wells and the second set of wells are physically distinguishable from each other by shape or dimension;

(b) determining sequence information for the sample nucleic acid template using signal data from the first well containing the sample nucleic acid template;

(c) constructing a phase-state model for a set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter that is determined using signal data from the plurality of other sample-containing wells, and wherein the model is stored in a machine-readable memory;

(d) calculating, using the phase-state model, predicted signals for the plurality of other sample-containing wells resulting from the set of nucleotide flows;

(e) comparing the predicted signals to the signal data from the plurality of other sample-containing wells;

(f) fitting the signal correction parameter of the phase-state model based on the comparison of the predicted signals to the signal data from the plurality of other sample-containing wells; and

(g) storing the fitted signal correction parameter in the memory.

2. The method of claim 1 , wherein the signal correction parameter is obtained using signal data obtained from at least a portion of the plurality of other sample-containing wells and without using signal data obtained from the first well.

3. The method of claim 1 , wherein the signal correction parameter is obtained using signal data obtained from at least a portion of the plurality of other sample-containing wells and signal data obtained from the first well.

4. The method of claim 1 , further comprising:

performing steps (b) through (g) for each of the obtained signal data from each or some of the plurality of other sample-containing wells to obtain multiple fitted signal correction parameters, wherein each of the multiple fitted signal correction parameters is determined for a given well without using signal data from that given well.

5. The method of claim 4 , wherein the comparing step comprises calculating a fitting metric that measures the fit between the predicted signals and the signal data.

6. The method of claim 1 , wherein the phase-state model includes two or more signal correction parameters, including a carry forward rate and an incomplete extension rate.

7. The method of claim 1 , wherein the comparing step comprises calculating a fitting metric that measures a fit between the predicted signals and the signal data.

8. The method of claim 7 , wherein the fitting step comprises determining a value of the signal correction parameter that optimizes the fitting metric.

9. The method of claim 7 , wherein the fitting step comprises determining a value of the signal correction parameter using Nelder-Mead optimization.

10. The method of claim 8 , wherein the fitting metric is calculated using only nucleotide flows that result in nucleotide non-incorporation or single nucleotide incorporations.

11. The method of claim 1 , further comprising performing a base calling analysis of the signal data using the fitted signal correction parameter.

12. The method of claim 1 , wherein the set of nucleotide flows is a first set of nucleotide flows and the sequence information is a first sequence information, and further comprising:

applying the phase-state model using the fitted signal correction parameter;

calculating, using the phase-state model and the fitted signal correction parameter obtained using signal data from the plurality of other sample-containing wells, predicted signals for the first well resulting from a second set of nucleotide flows that includes nucleotide flows that are not in the first set of nucleotide flows;

making base calls by comparing the signal data from the first well to the predicted signals for the first well; and

obtaining a second sequence information about the sample nucleic acid template, wherein the second sequence information includes sequence information not contained in the first sequence information.

13. The method of claim 12 , further comprising repeating steps (d) through (g) using the second sequence information to obtain a further fitted signal correction parameter.