Methods, systems, and computer readable media for making base calls in nucleic acid sequencing

A non-transitory machine-readable storage medium comprising instructions which, when executed by a processor, cause the processor to perform a method for nucleic acid sequencing comprising:

• a) for each of a plurality of defined spaces of a sensor array, receiving measurements of a parameter of a signal measured in response to a series of nucleotide flows flowed in the plurality of defined spaces, each defined space in an electrical communication with a sensor to provide the measurement of the signal generated in response to the nucleotide flow to the defined space, wherein sample nucleic acids are disposed in the defined spaces of the sensor array, wherein the series of nucleotide flows includes nucleotide species and polymerase;
• b) dividing the measurement of the signal generated by the sensor of the defined space in response to a nucleotide flow i by a reference value to produce a key-normalized measurement, wherein a plurality of key-normalized measurements corresponding to the series of nucleotide flows provides initial values for a plurality of normalized measurements;
• c) iteratively predicting a candidate base sequence and a plurality of predicted measurements corresponding to the candidate base sequence, comprising at each iteration:
• determining the candidate base sequence by applying one or more metrics that associate a score or a penalty to the candidate sequence of bases, wherein at least one of the metrics depends on a residual between the normalized measurement and the predicted measurement, wherein the residual comprises a difference between the predicted measurement and the normalized measurement, and
• generating the predicted measurements based on a simulation framework for modeling possible incorporations and non-incorporations of the nucleotide species, wherein the simulation framework includes possible states, state transitions and state transition parameters, wherein a first state of the possible states represents a non-incorporation of a particular base at a particular flow and a second state of the possible states represents an incorporation of the particular base at the particular flow by the polymerase associated with the sample nucleic acid;
• d) calculating a weighted average of ratios of the key-normalized measurements and the predicted measurements over a number N of the series of nucleotide flows, to determine a weighted average value for the N nucleotide flows;
• e) applying a normalization correction by dividing the key-normalized measurement of the signal corresponding to nucleotide flow i by a nominalization correction parameter to form the normalized measurement, wherein the normalization correction parameter is based on the weighted average value;
• and
• iteratively repeating steps c), d) and e), wherein the candidate base sequence produced at a final iteration of step c) provides a sequence of bases corresponding to the sample nucleic acid in the defined space.

A system, comprising:

• a machine-readable memory;
• and
• a processor configured to execute machine-readable instructions, which, when executed by the processor, cause the system to perform steps including:
• a) for each of a plurality of defined spaces of a sensor array, receiving measurements of a parameter of a signal measured in response to a series of nucleotide flows flowed in the plurality of defined spaces, each defined space in an electrical communication with a sensor to provide the measurement of the signal generated in response to the nucleotide flow to the defined space, wherein sample nucleic acids are disposed in the defined spaces of the sensor array, wherein the series of nucleotide flows includes nucleotide species and polymerase;
• b) dividing the measurement of the signal generated by the sensor of the defined space in response to a nucleotide flow i by a reference value to produce a key-nominalized measurement, wherein a plurality of key-normalized measurements corresponding to the series of nucleotide flows provides initial values for a plurality of normalized measurements;
• c) iteratively predicting a candidate base sequence and a plurality of predicted measurements corresponding to the candidate base sequence, comprising at each iteration:
• determining the candidate base sequence by applying one or more metrics that associate a score or a penalty to the candidate sequence of bases, wherein at least one of the metrics depends on a residual between the normalized measurement and the predicted measurement, wherein the residual comprises a difference between the predicted measurement and the normalized measurement, and
• generating the predicted measurements based on a simulation framework for modeling possible incorporations and non-incorporations of the nucleotide species, wherein the simulation framework includes possible states, state transitions and state transition parameters, wherein a first state of the possible states represents a non-incorporation of a particular base at a particular flow and a second state of the possible states represents an incorporation of the particular base at the particular flow by the polymerase associated with the sample nucleic acid;
• d) calculating a weighted average of ratios of the key-normalized measurements and the predicted measurements over a number N of the series of nucleotide flows, to determine a weighted average value for the N nucleotide flows;
• e) applying a normalization correction by dividing the key-normalized measurement of the signal corresponding to nucleotide flow i by a normalization correction parameter to form the normalized measurement, wherein the normalization correction parameter is based on the weighted average value;
• and
• iteratively repeating steps c), d) and e), wherein the candidate base sequence produced at a final iteration of step c) provides a sequence of bases corresponding to the sample nucleic acid in the defined space.