Methods, systems, and computer readable media for repeat sequencing

A system for sequencing a nucleic acid template, 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 a method comprising:
• (a) performing a first sequencing process on a first portion of the nucleic acid template to obtain a first sequencing result using a sequencing instrument configured to sequence a given sample two or more times, wherein the first sequencing process includes delivering first reagents including a first polymerase and first primers to the nucleic acid template and further includes flowing nucleotides to the nucleic acid template according to a first order comprising a first 4-flow block of flows comprising a first 4-flow permutation of flows A, C, G, and T, followed by a first predetermined number of repeats of a first 3-flow permutation of a first set of three flows selected from A, C, G, and T, followed by an isolated flow of the nucleotide not in the first set;
• and
• (b) after the first sequencing process, performing a second sequencing process on a second portion of the nucleic acid template to obtain a second sequencing result using the sequencing instrument, wherein the second sequencing process includes delivering second reagents including a second polymerase and second primers to the nucleic acid template and further includes flowing nucleotides to the nucleic acid template according to a second order different from the first order, wherein the first and second portions of the nucleic acid template may overlap at least partially, completely, or not at all.

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) performing a first sequencing process on a first portion of the nucleic acid template to obtain a first sequencing result using a sequencing instrument configured to sequence a given sample two or more times, wherein the first sequencing process includes delivering first reagents including a first polymerase and first primers to the nucleic acid template and further includes flowing nucleotides to the nucleic acid template according to a first order comprising a first 4-flow block of flows comprising a first 4-flow permutation of flows A, C, G, and T, followed by a first predetermined number of repeats of a first 3-flow permutation of a first set of three flows selected from A, C, G, and T, followed by an isolated flow of the nucleotide not in the first set, followed by a second 4-flow permutation of flows A, C, G, and T different than the first 4-flow permutation, followed by a second predetermined number of repeats of a second 3-flow permutation of a second set of three flows selected from A, C, G, and T different than the first set, followed by an isolated flow of the nucleotide not in the second set;
• and
• (b) after the first sequencing process, performing a second sequencing process on a second portion of the nucleic acid template to obtain a second sequencing result using the sequencing instrument, wherein the second sequencing process includes delivering second reagents including a second polymerase and second primers to the nucleic acid template and further includes flowing nucleotides to the nucleic acid template according to a second order different from the first order, wherein the first and second portions of the nucleic acid template may overlap at least partially, completely, or not at all.