System and method for correcting primer extension errors in nucleic acid sequence data

A method for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template nucleic acid molecule, comprising:

• (a) detecting a signal generated in response to an incorporation of one or more nucleotides in a sequencing reaction, wherein the signal is generated from the population of substantially identical copies of the template nucleic acid molecule;
• (b) generating a signal value for the signal;
• (c) incorporating the signal value into a representation associated with a sequence of a template nucleic acid molecule;
• (d) repeating steps (a)-(c) for a plurality of sequence positions of the template nucleic acid molecule;
• (e) correcting a plurality of the signal values for phasic synchrony error in the representation using a first parameter representative of an incomplete extension component of the phasic synchrony that comprises a measure of one or more of the substantially identical copies of the template nucleic acid molecules behind an extension phase of the population and a second parameter representative of a carry forward component of the phasic synchrony error that comprises a measure of one or more of the substantially identical copies of the template nucleic acid molecules ahead of the extension phase of the population;
• and
• (f) generating a corrected representation using the corrected signal values.

A method for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template nucleic acid molecule, comprising:

• (a) detecting a signal generated in response to an incorporation of one or more nucleotides in a sequencing reaction, wherein the signal is generated from the population of substantially identical copies of the template nucleic acid molecules;
• (b) generating a signal value for the signal;
• (c) incorporating the signal value into a representation associated with a sequence of the template nucleic acid molecule;
• (d) repeating steps (a)-(c) for a plurality of sequence positions of the template molecule;
• (e) dividing the representation into a plurality of sub-sets, wherein each sub-set comprises one or more of the sequence positions of the template molecule;
• (f) estimating a value for a first parameter representative of an incomplete extension component of a phasic synchrony error that comprises a measure of one or more of the substantially identical copies of the template nucleic acid molecules behind an extension phase of the population and a value for a second parameter representative of a carry forward component of the phasic synchrony error that comprises a measure of one or more of the substantially identical copies of the template nucleic acid molecules ahead of the extension phase of the population in each sub-set;
• (g) correcting the signal values in each sub-set for the phasic synchrony error using the estimations for the first parameter value and for the second parameter value for each respective sub-set;
• and
• (h) combining the corrected sub-sets into a corrected representation using the corrected signal values.

A system for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template nucleic acid molecule, comprising:

• a computer comprising program code stored for execution thereon, the program code performing a method comprising:
• (a) generating a value for a signal detected in response to an incorporation of one or more nucleotides in a sequencing reaction for a plurality of sequence positions of the template nucleic acid molecule, wherein the signal is generated from the population of substantially identical copies of the template nucleic acid molecules;
• and
• (b) correcting a plurality of the values for the plurality of sequence positions of the template nucleic acid molecule for a phasic synchrony error using a first parameter representative of an incomplete extension component of the phasic synchrony error that comprises a measure of one or more of the substantially identical copies of the template nucleic acid molecules behind an extension phase of the population and a second parameter representative of a carry forward component of the phasic synchrony error that comprises a measure of one or more of the substantially identical copies of the template nucleic acid molecules ahead of the extension phase of the population.

A system for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template nucleic acid molecule, comprising:

• a computer comprising program code stored for execution thereon, the program code performing a method comprising:
• (a) generating a value for a signal detected in response to an incorporation of one or more nucleotides in a sequencing reaction for a plurality of sequence positions of the template nucleic acid molecule, wherein the signal is generated from the population of substantially identical copies of the template nucleic acid molecules;
• (b) incorporating the value into a representation associated with a sequence of a template nucleic acid molecule;
• (c) repeating steps (a)-(b) for a plurality of sequence positions of the template nucleic acid molecule;
• (d) correcting a plurality of the values for phasic synchrony error in the representation using a first parameter representative of an incomplete extension component of the phasic synchrony error that comprises a measure of one or more of the substantially identical copies of the template nucleic acid molecules behind an extension phase of the population and a second parameter representative of a carry forward component of the phasic synchrony error that comprises a measure of one or more of the substantially identical copies of the template nucleic acid molecules ahead of the extension phase of the population;
• and
• (e) generating a corrected representation using the corrected values.

A system for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template nucleic acid molecule, comprising:

• a computer comprising program code stored for execution thereon, the program code performing a method comprising:
• (a) generating a value for a signal detected in response to an incorporation of one or more nucleotides in a sequencing reaction for a plurality of sequence positions of the template nucleic acid molecule, wherein the signal is generated from the population of substantially identical copies of the template nucleic acid molecules;
• (b) incorporating the value into a representation associated with a sequence of the template nucleic acid molecule;
• (c) repeating steps (a)-(c) for a plurality of sequence positions of the template molecule;
• (d) dividing the representation into a plurality of sub-sets, wherein each sub-set comprises one or more of the sequence positions of the template molecule;
• (e) estimating a value for a first parameter representative of an incomplete extension component of a phasic synchrony error that comprises a measure of one or more of the substantially identical copies of the template nucleic acid molecules behind an extension phase of the population and a value for a second parameter representative of a carry forward component of the phasic synchrony error that comprises a measure of one or more of the substantially identical copies of the template nucleic acid molecules ahead of the extension phase of the population in each sub-set;
• (f) correcting the signal values in each sub-set for the phasic synchrony error using the estimations for the first parameter value and for the second parameter value for each respective sub-set;
• and
• (g) combining the corrected sub-sets into a corrected representation using the corrected values.