Methods and systems for modeling phasing effects in sequencing using termination chemistry

A nucleic acid sequencing system, comprising:

• a sequencing instrument configured to receive a sample nucleic acid, at least one nucleotide having a terminating group, a primer, and a polymerase, and to subject the sample nucleic acid to a sequencing-by-synthesis assay to produce raw sequencing data from detecting electrical changes resulting from hydrogen ions released from incorporation of nucleotide species during the sequencing-by-synthesis assay, wherein the sequencing-by-synthesis assay comprises a total number of nucleotide flows greater than about 160;
• and
• a processor configured to:
• receive the raw sequencing data,
• use a simulation model to generate predicted sequencing data, wherein the simulation model comprises:
• determining a simulation framework for simulating possible state transitions for active and inactive molecules present at a K-th base during an N-th nucleotide flow in a termination sequencing-by-synthesis assay, where K and N denote indices associated with bases and the nucleotide flows, respectively, wherein the simulation framework for simulating the possible state transitions incorporates:
• an estimated carry forward rate (CFR),
• an estimated termination incomplete extension rate (TER),
• an estimated droop rate (DR),
• an estimated reactivated molecules rate (RMR) greater than or equal to zero, and
• an estimated termination failure rate (TFR) less than one,
• compare the raw sequencing data with the predicted sequencing data;
• and
• based on the comparison of the raw sequencing data with the predicted sequencing data, output a candidate sequence for the sample nucleic acid.

An apparatus, comprising:

• a machine-readable memory;
• and
• a processor configured to execute machine-readable instructions, the instructions which when executed cause the apparatus to:
• generating raw sequencing data obtained from detecting electrical changes resulting from release of hydrogen ions from incorporation of nucleotide species during sequencing of a sample nucleic acid using a sequencing-by-synthesis assay comprising a total number of nucleotide flows greater than about 160, the raw sequencing data comprising one or more phasing errors;
• use a simulation model to generate predicted sequencing data, wherein the simulation model comprises:
• a simulation framework simulating possible state transitions for active and inactive molecules present at a K-th base during an N-th nucleotide flow in a termination sequencing-by-synthesis assay, where K and N denote indices associated with bases and the nucleotide flows, respectively, wherein the simulation framework incorporates:
• an estimated carry forward rate (CFR),
• an estimated termination incomplete extension rate (TER),
• an estimated droop rate (DR),
• an estimated reactivated molecules rate (RMR) greater than or equal to zero, and
• an estimated termination failure rate (TFR) less than one;
• compare the raw sequencing data with the predicted sequencing data;
• and
• based on the comparison of the raw sequencing data with the predicted sequencing data, output a candidate sequence for the sample nucleic acid.