Methods and computer program products for compression of sequencing data

Abstract

A compression method includes measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises at least one region associated with expected measured values and at least one region associated with unpredictable measured values; applying a first compression process to the waveform, the first compression process including an averaging of one or more frames in one or more portions of the waveform; applying a keyframe delta compression to the frame-averaged data; forming a compressed data structure including a keyframe and calculated differences subsequent to the keyframe; and storing one or more compressed data structures in memory.

1 .- 20 . (canceled) 
     
     
         21 . A compression method, comprising:
 measuring a waveform associated with a chemical event occurring on a sensor array, the measuring including digitizing voltage signals using an analog to digital converter to produce a plurality of frames of measured values for the waveform, the voltage signals generated by the sensor array in response to the chemical event, wherein the chemical event is indicative of a number of nucleotide incorporations in a genetic sequencing reaction, wherein the waveform comprises at least one portion associated with expected measured values and at least one portion associated with unpredictable measured values;   applying a first compression process to the waveform using a processor, the first compression process including an averaging of one or more frames in one or more portions of the waveform to form frame-averaged data, wherein a number of frames of the frame-averaged data is less than a number of frames in the plurality of frames of measured values;   applying a keyframe delta compression to the frame-averaged data using the processor, wherein the keyframe delta compression comprises calculating a difference between a current frame of the frame-averaged data and a previous frame of the frame-averaged data associated with the waveform;   forming a compressed data structure including a keyframe of the frame-averaged data and a plurality of the calculated differences subsequent to the keyframe, wherein the compressed data structure represents the keyframe and the plurality calculated differences in a number of bytes that is less than an original number of bytes representing the frame-averaged data; and   storing one or more compressed data structures in a memory.   
     
     
         22 . The method of  claim 21 , further comprising:
 determining compression information corresponding to the one or more compressed data structures; and   storing the compression information in the memory.   
     
     
         23 . The method of  claim 22 , wherein the compression information includes the number of bytes for storing each of the one or more compressed data structures. 
     
     
         24 . The method of  claim 23 , wherein the compression information includes a code indicating a change in the number of bytes for storing the one or more compressed data structures from a previous compressed data structure. 
     
     
         25 . The method of  claim 21 , wherein the averaging comprises:
 applying a first frame averaging to the at least one portion associated with the expected measured values, wherein the first frame averaging comprises averaging a first number of frames during the at least one portion associated with the expected measured values; and   applying a second frame averaging to the at least one portion associated with the unpredictable measured values, wherein the second frame averaging comprises averaging a second number of frames during the at least one portion associated with the unpredictable measured values, the second number of frames being lower than the first number of frames.   
     
     
         26 . The method of  claim 25 , further comprising:
 applying a third frame averaging to a second portion of the waveform, wherein the second portion is associated with another portion of the waveform with expected measured values, and wherein the third frame averaging comprises averaging a third number of frames during the second portion, the third number of frames being higher than the second number of frames.   
     
     
         27 . The method of  claim 21 , wherein the measuring the waveform comprises measuring the waveform of a dynamic response of an ion-sensitive field effect transistor (ISFET) array to a change in ionic strength of an analyte solution in fluid contact with the ISFET array. 
     
     
         28 . The method of  claim 27 , wherein the measuring the waveform of the dynamic response of the ISFET array comprises associating the at least one portion with the unpredictable measured values to a stepwise increase in ion concentration in the analyte solution and associating the at least one portion with the expected measured values to at least one portion of the dynamic response outside of the stepwise increase in ion concentration. 
     
     
         29 . The method of  claim 28 , wherein the averaging comprises applying a first frame averaging to the at least one portion associated with the expected measured values, wherein the first frame averaging comprises averaging a first number of frames during the at least one portion associated with the expected measured values, wherein the first number of frames results from measured values during the at least one portion of the dynamic response outside of the stepwise increase in ion concentration. 
     
     
         30 . The method of  claim 28 , wherein the averaging comprises applying a second frame averaging to the at least one portion associated with the unpredictable measured values, wherein the second frame averaging comprises averaging a second number of frames during the at least one portion associated with the unpredictable measured values, wherein the second number of frames results from measured values during the stepwise increase in ion concentration in the analyte solution. 
     
     
         31 . A computer program product comprising a computer-usable medium having computer program logic recorded thereon that, when executed by one or more processors, compresses data from a sensor array, wherein the data comprise digitized voltage signals generated by the sensor array in response to a chemical event occurring on the sensor array to produce a plurality of frames of measured values of a waveform, wherein the chemical event is indicative of a number of nucleotide incorporations in a genetic sequencing reaction, the computer program logic comprising computer readable program code that enables a processor to:
 obtain the plurality of frames of measured values of the waveform associated with the chemical event occurring on the sensor array, wherein the waveform comprises at least one portion associated with expected measured values and at least one portion associated with unpredictable measured values;   apply a first compression process to the waveform, the first compression process including an averaging of one or more frames in one or more portions of the waveform to form frame-averaged data, wherein a number of frames of the frame-averaged data is less than a number of frames in the plurality of frames of measured values;   apply a keyframe delta compression to the frame-averaged data, wherein the keyframe delta compression comprises calculating a difference between a current frame of the frame-averaged data and a previous frame of the frame-averaged data associated with the waveform;   form a compressed data structure including a keyframe of the frame-averaged data and a plurality of the calculated differences subsequent to the keyframe, wherein the compressed data structure represents the keyframe and the plurality calculated differences in a number of bytes that is less than an original number of bytes representing the frame-averaged data; and   store one or more compressed data structures in a memory.   
     
     
         32 . The computer program product of  claim 31 , wherein the computer readable program code enables the processor to:
 determine compression information corresponding to the one or more compressed data structures, and   store the compression information in the memory.   
     
     
         33 . The computer program product of  claim 32 , wherein the compression information includes the number of bytes for storing each of the one or more compressed data structures. 
     
     
         34 . The computer program product of  claim 33 , wherein the compression information includes a code indicating a change in the number of bytes for storing the one or more compressed data structures from a previous compressed data structure. 
     
     
         35 . The computer program product of  claim 31 , wherein the computer readable program code for the first compression process enables the processor to:
 apply a first frame averaging to the at least one portion associated with the expected measured values, wherein the first frame averaging comprises averaging a first number of frames during the at least one portion associated with the expected measured values, and   apply a second frame averaging to the at least one portion associated with the unpredictable measured values, wherein the second frame averaging comprises averaging a second number of frames during the at least one portion associated with the unpredictable measured values, the second number of frames being lower than the first number of frames.   
     
     
         36 . The computer program product of  claim 35 , wherein the computer readable program code for the first compression process enables the processor to:
 apply a third frame averaging to a second portion of the waveform, wherein the second portion is associated with another portion of the waveform with expected measured values, and wherein the third frame averaging comprises averaging a third number of frames during the second portion, the third number of frames being higher than the second number of frames.   
     
     
         37 . The computer program product of  claim 31 , wherein the sensor array comprises an ion-sensitive field effect transistor (ISFET) array that generates a dynamic response to a change in ionic strength of an analyte solution in fluid contact with the ISFET array. 
     
     
         38 . The computer program product of  claim 37 , wherein the computer readable program code enables the processor to associate the at least one portion with the unpredictable measured values to a stepwise increase in ion concentration in the analyte solution and associating the at least one portion with the expected measured values to at least one portion of the dynamic response outside of the stepwise increase in ion concentration. 
     
     
         39 . The computer program product of  claim 38 , wherein the computer readable program code enables the processor to apply a first frame averaging to the at least one portion associated with the expected measured values, wherein the first frame averaging comprises averaging a first number of frames during the at least one portion associated with the expected measured values, wherein the first number of frames results from measured values during the at least one portion of the dynamic response outside of the stepwise increase in ion concentration. 
     
     
         40 . The computer program product of  claim 38 , wherein the computer readable program code enables the processor to apply a second frame averaging to the at least one portion associated with the unpredictable measured values, wherein the second frame averaging comprises averaging a second number of frames during the at least one portion associated with the unpredictable measured values, wherein the second number of frames results from measured values during the stepwise increase in ion concentration in the analyte solution.