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 sequence information, comprising:
 obtaining first and second sequence signal information for a polynucleotide, the first and second sequence signal information derived from sequencing at least partially overlapping regions of the polynucleotide;   aligning at least a portion of the first and second sequence signal information;   determining, with a processor, a degree of agreement between the first and second sequence signal information for a location along the polynucleotide;   determining, with a processor, a weighted average signal for the location based on the first and second sequence signal information; and   determining, with a processor, a base call and quality value for the location based on the weighted average signal and the degree of agreement.   
     
     
         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 sequence signal information is flow space information. 
     
     
         4 . The method of  claim 1 , wherein the weighted average signal is determined in part based on the relative locations within the first and second sequence signal information. 
     
     
         5 . The method of  claim 1 , wherein the quality value is higher for a location with a higher degree of agreement than for a location with a lower degree of agreement. 
     
     
         6 . The method of  claim 1 , wherein the degree of agreement is based on an agreement between an initial base call from the first sequence signal information and an initial base call from the second sequence signal information. 
     
     
         7 . A system for analyzing overlapping sequence information, comprising:
 a processor configured to:   obtain first and second sequence signal information for a polynucleotide, the first and second sequence signal information derived from sequencing at least partially overlapping regions of the polynucleotide;   align at least a portion of the first and second sequence signal information;   determine a degree of agreement between the first and second sequence signal information for a location along the polynucleotide;   determine a weighted average signal for the location based on the first and second sequence signal information; and   determine a base call and quality value for the location based on the weighted average signal and the degree of agreement.   
     
     
         8 . The system of  claim 6 , wherein the sequence signal information is flow space information. 
     
     
         9 . The system of  claim 6 , wherein the processor is configured to determine the weighted average signal at least in part based on the relative locations within the first and second sequence signal information. 
     
     
         10 . The system of  claim 6 , wherein the processor is configured to determine a higher quality value for a location with a higher degree of agreement than for a location with a lower degree of agreement. 
     
     
         11 . The system of  claim 6 , wherein the degree of agreement is based on an agreement between an initial base call from the first sequence signal information and an initial base call from the second sequence signal information. 
     
     
         12 - 16 . (canceled) 
     
     
         17 . 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.   
     
     
         18 . The method of  claim 17 , wherein sequencing in the first direction includes extending a first primer in the first direction. 
     
     
         19 . The method of  claim 18 , further comprising removing a portion of the target nucleic acid after sequencing in the first direction, leaving the extended first primer and a portion of the target nucleic acid to act as a second primer. 
     
     
         20 . The method of  claim 19 , wherein sequencing in the second direction includes extending the second primer in the second direction. 
     
     
         21 . The method of  claim 17 , wherein the sequence signal information is flow space information. 
     
     
         22 . The method of  claim 17 , wherein the weighted average signal is determined in part based on the relative locations within the first and second sequence signal information. 
     
     
         23 . The method of  claim 17 , wherein the quality value is higher for a location with a higher degree of agreement than for a location with a lower degree of agreement. 
     
     
         24 . The method of  claim 17 , wherein the degree of agreement is based on an agreement between an initial base call from the first sequence signal information and an initial base call from the second sequence signal information.