A method for nucleic acid sequencing, comprising: disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith; exposing the template polynucleotide strands with the sequencing primer and a polymerase operably bound therewith to a series of flows of nucleotide species flowed according to a predetermined ordering; and determining, for each of the series of flows of nucleotide species, how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands, wherein the predetermined ordering: (a) is not a series of consecutive repetitions of a 4- flow permutation of four different nucleotide species, and (b) comprises a phase-protecting flow ordering that comprises a de Bruijn sequence of nucleotide species A, C, G and T such that: (i) every possible subsequence of two of the nucleotide species A, C, G and T appears once as a sequence of consecutive nucleotide species in the de Bruijn sequence or (ii) every possible subsequence of three of the nucleotide species A, C, G and T appears once as a sequence of consecutive nucleotide species in the de Bruijn sequence. disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith; exposing the template polynucleotide strands with the sequencing primer and a polymerase operably bound therewith to a series of flows of nucleotide species flowed according to a predetermined ordering; and determining, for each of the series of flows of nucleotide species, how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands, wherein the predetermined ordering: (a) is not a series of consecutive repetitions of a 4- flow permutation of four different nucleotide species, and (b) comprises a phase-protecting flow ordering that comprises a de Bruijn sequence of nucleotide species A, C, G and T such that: (i) every possible subsequence of two of the nucleotide species A, C, G and T appears once as a sequence of consecutive nucleotide species in the de Bruijn sequence or (ii) every possible subsequence of three of the nucleotide species A, C, G and T appears once as a sequence of consecutive nucleotide species in the de Bruijn sequence. (a) is not a series of consecutive repetitions of a 4- flow permutation of four different nucleotide species, and (b) comprises a phase-protecting flow ordering that comprises a de Bruijn sequence of nucleotide species A, C, G and T such that: (i) every possible subsequence of two of the nucleotide species A, C, G and T appears once as a sequence of consecutive nucleotide species in the de Bruijn sequence or (ii) every possible subsequence of three of the nucleotide species A, C, G and T appears once as a sequence of consecutive nucleotide species in the de Bruijn sequence. (i) every possible subsequence of two of the nucleotide species A, C, G and T appears once as a sequence of consecutive nucleotide species in the de Bruijn sequence or (ii) every possible subsequence of three of the nucleotide species A, C, G and T appears once as a sequence of consecutive nucleotide species in the de Bruijn sequence.