Systems and methods for paired end sequencing
AssigneeLife Technologies Corporation
InventorsSowmi UTIRAMERUR, Simon CAWLEY, Yongming SUN, Fiona HYLAND
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Abstract
Systems and methods for analyzing overlapping sequence information can obtain first and second overlapping sequence information for a polynucleotide, align the first and second sequence information, determine a degree of agreement between the first and second sequence information for a location along the polynucleotide, and determine a base call and a quality value for the location.
Claims20
A method of analyzing overlapping read sequences of a polynucleotide produced by a nucleic acid sequencing platform, comprising:
- obtaining, at a processor, first and second sequence signal information for the polynucleotide, the first and second sequence signal information derived from first and second signals detected by a sensor in response to nucleotide incorporations for sequencing at least partially overlapping regions of the polynucleotide;
- comparing at least a portion of the first and second sequence signal information to align an overlapping region of the first and second sequence signal information;
- comparing respective values of the first and second sequence signal information for a position in the overlapping region to indicate concordance or discordance;
- when discordance is indicated for the position, calculating a weighted average of the respective values of the first and second sequence signal information for the position to form a weighted average signal, wherein respective weights are applied to the respective values;
- determining a base call and a quality value for the position, wherein the base call and quality value are based on the weighted average signal when discordance is indicated for the position;
- and
- providing a sequence of base calls and quality values corresponding to the positions in the overlapping region.
A system for analyzing overlapping read sequences of a polynucleotide produced by a nucleic acid sequencing platform, comprising:
- a processor, the processor configured to:
- obtain first and second sequence signal information for the polynucleotide, the first and second sequence signal information derived from first and second signals detected by a sensor in response to nucleotide incorporations for sequencing at least partially overlapping regions of the polynucleotide;
- compare at least a portion of the first and second sequence signal information to align an overlapping region of the first and second sequence signal information;
- compare respective values of the first and second sequence signal information for a position in the overlapping region to indicate concordance or discordance;
- when discordance is indicated for the position, calculate a weighted average of the respective values of the first and second sequence signal information for the position to form a weighted average signal, wherein respective weights are applied to the respective values;
- determine a base call and a quality value for the position, wherein the base call and quality value are based on the weighted average signal when discordance is indicated for the position;
- and
- provide a sequence of base calls and quality values corresponding to the positions in the overlapping region.
A method of analyzing overlapping sequence information, comprising:
- sequencing a target nucleic acid in a first direction to obtain a first sequence signal information;
- sequencing the target nucleic acid in a second direction to obtain a second sequence signal information;
- aligning at least a portion of the first and second sequence signal information;
- determining a degree of agreement between the first and second sequence signal information for a location along the polynucleotide;
- determining a weighted average signal for the location based on the first and second sequence signal information;
- and
- determining a base call and quality value for the location based on the weighted average signal and the degree of agreement.
Dependencies are inferred from the claim text.