Pulse caller and base caller

Abstract

System and methods for identifying nucleotides based on data acquired from a sensor during sequencing of nucleic acids. The method may include obtaining characteristics of light detected from luminescent labels associated with the nucleotides during nucleotide incorporation events. The characteristics may include, for each nucleotide incorporation event, a temporal characteristic the light and an intensity characteristic of the light. The temporal characteristic representing a speed of decay of a probability of photon emission by a luminescent label after excitation. The method may further include grouping points representing the characteristics of the nucleotide incorporation events into groups of points. The individual points may represent at least the temporal characteristic and the intensity characteristic for a corresponding nucleotide incorporation event. The method may further include assigning the groups of points to individual nucleotides.

What is claimed is: 
     
         1 .- 35 . (canceled) 
     
     
         36 . A sequencing method, comprising:
 obtaining, by a processor, characteristics of light received by a photodetector from luminescent labels during nucleotide incorporation events of a sequencing reaction, the luminescent labels being associated with nucleotides, the characteristics including, for individual nucleotide incorporation events,
 a temporal characteristic of the light, the temporal characteristic representing a speed of decay of a probability of photon emission by a luminescent label after excitation; and 
 an intensity characteristic of the light, wherein the temporal characteristic and the intensity characteristic are characteristics of light received from a luminescent label during a nucleotide incorporation event; and 
   wherein the temporal characteristic and the intensity characteristic are used to perform one or more of: identifying individual nucleotides, and calibrating a sequencing instrument, and   wherein the intensity characteristic represents a quantity of photogenerated charge carriers produced over time by the photodetector from the light received from the luminescent label during the nucleotide incorporation event.   
     
     
         37 . The sequencing method of  claim 36 , wherein the temporal characteristic and the intensity characteristic are used to perform identifying individual nucleotides, and wherein the identifying of the individual nucleotides comprises:
 grouping points representing the characteristics into groups of points, individual points representing at least the temporal characteristic and the intensity characteristic for a corresponding nucleotide incorporation event; and   assigning the groups of points to individual nucleotides.   
     
     
         38 . The sequencing method of  claim 37 , wherein the points are grouped using a clustering algorithm. 
     
     
         39 . The sequencing method of  claim 38 , wherein the clustering algorithm performs k-means clustering in which k is greater than or equal to four. 
     
     
         40 . The sequencing method of  claim 38 , wherein the groups of points are assigned to the individual nucleotides based on predetermined light-emitting characteristics of the luminescent labels. 
     
     
         41 . The sequencing method of  claim 37 , wherein the temporal characteristic and the intensity characteristic are used to perform identifying individual nucleotides, and wherein the identifying of the individual nucleotides comprises:
 determining one or more criteria distinguishing groups of points representing the characteristics, individual points representing the temporal characteristic and the intensity characteristic for a corresponding nucleotide incorporation event;   assigning the groups to respective nucleotides to produce nucleotide assignments for the groups; and   assigning the points to nucleotides based on the one or more criteria and the nucleotide assignments for the groups.   
     
     
         42 . The sequencing method of  claim 36 , wherein the temporal characteristic and the intensity characteristic are used to perform identifying individual nucleotides, wherein the identifying of the individual nucleotides comprises assigning the nucleotide incorporation events to nucleotides by evaluating the temporal characteristic and the intensity characteristic in view of stored criteria for the sequencing instrument, and distinguishing between the characteristics of the light for the luminescent labels. 
     
     
         43 . The sequencing method of  claim 42 , wherein the stored criteria comprises one or more boundaries between characteristics of the luminescent labels for different nucleotides, and the assigning of the nucleotide incorporation events comprises comparing a point representing the temporal characteristic and the intensity characteristic with the one or more boundaries. 
     
     
         44 . The sequencing method of  claim 42 , wherein the stored criteria comprises centroids of groups of points, each group corresponding to a respective nucleotide, and the assigning of the nucleotide incorporation events comprises:
 determining distances between a point representing the temporal characteristic and the intensity characteristic for an incorporation event to the centroids; and   assigning the nucleotide incorporation event to a nucleotide with a centroid closest to the point.   
     
     
         45 . The sequencing method of  claim 37 , wherein the temporal characteristic and the intensity characteristic are used to perform identifying of individual nucleotides, wherein the identifying the individual nucleotides comprises:
 determining one or more criteria distinguishing groups of points representing the characteristics of the nucleotide incorporation events, individual points representing the temporal characteristic and the intensity characteristic for a corresponding nucleotide incorporation event;   assigning the groups to respective nucleotides to produce nucleotide assignments for the groups; and   assigning the points to nucleotides based on the one or more criteria and the nucleotide assignments for the groups.   
     
     
         46 . A non-transitory computer readable storage medium having stored thereon instructions, which, when executed by a processor, performs a sequencing method, comprising:
 obtaining, by a processor, characteristics of light received by a photodetector from luminescent labels during nucleotide incorporation events of a sequencing reaction, the luminescent labels being associated with nucleotides, the characteristics including, for individual nucleotide incorporation events,
 a temporal characteristic of the light, the temporal characteristic representing a speed of decay of a probability of photon emission by a luminescent label after excitation; and 
 an intensity characteristic of the light, wherein the temporal characteristic and the intensity characteristic are characteristics of light received from a luminescent label during a nucleotide incorporation event; and 
   wherein the temporal characteristic and the intensity characteristic are used to perform one or more of: identifying individual nucleotides, and calibrating a sequencing instrument, and   wherein the intensity characteristic represents a quantity of photogenerated charge carriers produced over time by the photodetector from the light received from the luminescent label during the nucleotide incorporation event.   
     
     
         47 . The non-transitory computer readable storage medium of  claim 46 , wherein the temporal characteristic and the intensity characteristic are used to perform identifying individual nucleotides, and wherein the identifying of the individual nucleotides comprises:
 grouping points representing the characteristics into groups of points, individual points representing at least the temporal characteristic and the intensity characteristic for a corresponding nucleotide incorporation event; and   assigning the groups of points to individual nucleotides.   
     
     
         48 . The non-transitory computer readable storage medium of  claim 47 , wherein the points are grouped using a clustering algorithm. 
     
     
         49 . The non-transitory computer readable storage medium of  claim 48 , wherein the clustering algorithm performs k-means clustering in which k is greater than or equal to four. 
     
     
         50 . The non-transitory computer readable storage medium of  claim 48 , wherein the groups of points are assigned to the individual nucleotides based on predetermined light-emitting characteristics of the luminescent labels. 
     
     
         51 . The non-transitory computer readable storage medium of  claim 47 , wherein the temporal characteristic and the intensity characteristic are used to perform identifying individual nucleotides, and wherein the identifying of the individual nucleotides comprises:
 determining one or more criteria distinguishing groups of points representing the characteristics, individual points representing the temporal characteristic and the intensity characteristic for a corresponding nucleotide incorporation event;   assigning the groups to respective nucleotides to produce nucleotide assignments for the groups; and   assigning the points to nucleotides based on the one or more criteria and the nucleotide assignments for the groups.   
     
     
         52 . The non-transitory computer readable storage medium of  claim 46 , wherein the temporal characteristic and the intensity characteristic are used to perform identifying individual nucleotides, wherein the identifying of the individual nucleotides comprises assigning the nucleotide incorporation events to nucleotides by evaluating the temporal characteristic and the intensity characteristic in view of stored criteria for the sequencing instrument, and distinguishing between the characteristics of the light for the luminescent labels. 
     
     
         53 . The non-transitory computer readable storage medium of  claim 52 , wherein the stored criteria comprises one or more boundaries between characteristics of the luminescent labels for different nucleotides, and the assigning of the nucleotide incorporation events comprises comparing a point representing the temporal characteristic and the intensity characteristic with the one or more boundaries. 
     
     
         54 . The non-transitory computer readable storage medium of  claim 52 , wherein the stored criteria comprises centroids of groups of points, each group corresponding to a respective nucleotide, and the assigning of the nucleotide incorporation events comprises:
 determining distances between a point representing the temporal characteristic and the intensity characteristic for an incorporation event to the centroids; and   assigning the nucleotide incorporation event to a nucleotide with a centroid closest to the point.   
     
     
         55 . The non-transitory computer readable storage medium of  claim 47 , wherein the temporal characteristic and the intensity characteristic are used to perform identifying of individual nucleotides, wherein the identifying the individual nucleotides comprises:
 determining one or more criteria distinguishing groups of points representing the characteristics of the nucleotide incorporation events, individual points representing the temporal characteristic and the intensity characteristic for a corresponding nucleotide incorporation event;   assigning the groups to respective nucleotides to produce nucleotide assignments for the groups; and   assigning the points to nucleotides based on the one or more criteria and the nucleotide assignments for the groups.