Systems and methods for paired end sequencing

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.

1 . 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.   
     
     
         2 . The method of  claim 1 , wherein obtaining the first and second sequence signal information includes sequencing a target nucleic acid while extending a first primer in a first direction, and sequencing the target nucleic acid while extending a second primer in a second direction opposite the first direction. 
     
     
         3 . The method of  claim 1 , wherein the first and second sequence signal information comprise first and second flow space information. 
     
     
         4 . The method of  claim 1 , wherein the respective weights are based on respective accuracies of the first and second sequence signal information for the position. 
     
     
         5 . The method of  claim 1 , wherein the quality value is higher for a position where concordance is indicated than for a position where discordance is indicated. 
     
     
         6 . The method of  claim 1 , wherein the comparing respective values comprises comparing an initial base call from the first sequence signal information and an initial base call from the second sequence signal information for the position. 
     
     
         7 . The method of  claim 3 , wherein the comparing at least a portion of the first and second flow space information further comprises:
 obtaining, at the processor, first and second initial base sequences corresponding to the first and second sequence signal information; and   comparing respective bases of the first and second initial base sequences to align an overlapping region of the first and second initial base sequences to produce first and second aligned base sequences.   
     
     
         8 . The method of  claim 7 , further comprising mapping values of the first and second flow space information to corresponding bases in the overlapping region of the first and second aligned base sequences to align the overlapping region of the first and second sequence signal information. 
     
     
         9 . The method of  claim 7 , further comprising inserting empty flow information into the first and second aligned base sequences using corresponding flow order information. 
     
     
         10 . 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.   
     
     
         11 . The system of  claim 10 , wherein the first and second sequence signal information comprise first and second flow space information. 
     
     
         12 . The system of  claim 10 , wherein the respective weights are based on respective accuracies of the first and second sequence signal information for the position. 
     
     
         13 . The system of  claim 10 , wherein the quality value is higher for a position where concordance is indicated than for a position where discordance is indicated. 
     
     
         14 . The system of  claim 10 , wherein to compare respective values, the processor is configured to compare an initial base call from the first sequence signal information and an initial base call from the second sequence signal information for the position. 
     
     
         15 . The system of  claim 11 , wherein to compare at least a portion of the first and second sequence signal information, the processor is further configured to:
 obtain first and second initial base sequences corresponding to the first and second sequence signal information; and   compare respective bases of the first and second initial base sequences to align an overlapping region of the first and second initial base sequences to produce first and second aligned base sequences.   
     
     
         16 . The system of  claim 15 , wherein the processor is configured to map values of the first and second flow space information to corresponding bases in the overlapping region of the first and second aligned base sequences to align the overlapping region of the first and second sequence signal information. 
     
     
         17 . The system of  claim 15 , the processor is configured to insert empty flow information into the first and second aligned base sequences using corresponding flow order information. 
     
     
         18 .- 20 . (canceled)