A method for nucleic acid sequencing, comprising: receiving observed or measured nucleic acid sequencing data from a sequencing instrument configured to receive a sample nucleic acid and to process the sample nucleic acid in a termination sequencing-by-synthesis process; generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for each candidate sequence of the set of candidate sequences using a simulation framework for simulating possible molecule states and state transitions for active and inactive molecules present at a K-th base during an N-th nucleotide flow, where K and N denote indices associated with bases and nucleotide flows, respectively, wherein the simulation framework for simulating the possible state transitions incorporates an estimated carry forward rate, CFR, an estimated incomplete extension rate, IER, an estimated droop rate, DR, an estimated reactivated molecules rate, RMR, corresponding to a rate at which inactive nucleic acid copies become reactivated at a later point in time than intended, and an estimated termination failure rate, TFR, corresponding to a rate at which phasing errors occur due to ineffective termination of primer extension, the RMR being greater than zero and the TFR being lesser than one; and identifying, from the set of candidate sequences of bases, one candidate sequence leading to optimization of a solver function as corresponding to the sequence for the sample nucleic acid by determining which sequence is most consistent with the observed or measured nucleic acid sequencing data. receiving observed or measured nucleic acid sequencing data from a sequencing instrument configured to receive a sample nucleic acid and to process the sample nucleic acid in a termination sequencing-by-synthesis process; generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for each candidate sequence of the set of candidate sequences using a simulation framework for simulating possible molecule states and state transitions for active and inactive molecules present at a K-th base during an N-th nucleotide flow, where K and N denote indices associated with bases and nucleotide flows, respectively, wherein the simulation framework for simulating the possible state transitions incorporates an estimated carry forward rate, CFR, an estimated incomplete extension rate, IER, an estimated droop rate, DR, an estimated reactivated molecules rate, RMR, corresponding to a rate at which inactive nucleic acid copies become reactivated at a later point in time than intended, and an estimated termination failure rate, TFR, corresponding to a rate at which phasing errors occur due to ineffective termination of primer extension, the RMR being greater than zero and the TFR being lesser than one; and identifying, from the set of candidate sequences of bases, one candidate sequence leading to optimization of a solver function as corresponding to the sequence for the sample nucleic acid by determining which sequence is most consistent with the observed or measured nucleic acid sequencing data.