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1. (WO2018068014) SYSTEM AND METHOD FOR SECONDARY ANALYSIS OF NUCLEOTIDE SEQUENCING DATA
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WHAT IS CLAIMED IS:

1. A system for sequencing polynucleotides:

a memory comprising a reference nucleotide sequence;

a processor configured to execute instructions that perform a method comprising:

receiving a first nucleotide subsequence of a read from a sequencing system;

processing the first nucleotide subsequence using a first alignment path to determine a first plurality of candidate locations of the read on the reference sequence;

determining whether the first nucleotide subsequence aligns to the reference sequence based on the determined candidate locations;

receiving a second nucleotide subsequence from the sequencing system;

processing the second nucleotide subsequence to determine a second plurality of candidate locations of the read that align to the reference sequence using:

a second alignment path if the read is aligned to the reference sequence, and

the first alignment path if otherwise,

wherein the second alignment path is more computationally efficient than the first alignment path to determine the second plurality of candidate locations of the read.

2. The system of claim 1, wherein the second nucleotide subsequence is processed using the first alignment path or the second alignment path based on an alignment quality metric.

3. The system of claim 1, wherein the first nucleotide subsequence is one or more nucleotides in length.

4. The system of claim 1, wherein the second nucleotide subsequence is one or more nucleotides in length.

5. The system of claim 1, wherein the second alignment path is more computationally efficient than the first alignment path in memory usage or the number of computation operations.

6. The system of claim 1 wherein the processor is further configured to store data corresponding to at least one of the first plurality of candidate locations if the first nucleotide subsequence is aligned to the reference sequence.

7. The system of claim 6 wherein the processor is further configured to store data corresponding to at least one of the second plurality of candidate locations if the read remains aligned to the reference sequence.

8. The system of claim 1, wherein processing the second nucleotide subsequence using the second alignment path comprises performing a simple alignment to determine a simple alignment score.

9. The system of claim 8, wherein performing the simple alignment comprises comparing the second nucleotide subsequence with corresponding sequences of the second nucleotide subsequence on the reference sequence based on the first plurality of candidate positions.

10. The system of claim 8, wherein processing the second nucleotide subsequence using second processing path further comprises determining a mapping quality (MapQ) score for each of the second plurality of candidate locations of the read.

11. The system of claim 10, wherein the simple alignment score comprises the MapQ score.

12. The system of claim 1, wherein the processor is further configured to perform variant calling on the output of the first or second alignment path comprising at least one of the first plurality of candidate locations or at least one of the second plurality of candidate locations.

13. The system of claim 12, wherein performing the variant calling on the output of the first or second alignment path comprises:

performing variant calling on the output of the first or second alignment path using a first variant calling path or a second variant calling path, wherein the second variant calling path is more computationally efficient than the first variant calling path in variant calling of the second subsequence.

14. The system of claim 12, wherein the variant calling is performed using the output of the first or second alignment path based on a variant calling metric.

15. The system of claim 14, wherein the variant calling metric is determined based on a number of different base types called at a position of the reference sequence.

16. The system of claim 1, wherein processing the first nucleotide subsequence is completed before the sequencing system determines the second nucleotide subsequence during a sequencing run.

17. The system of claim 1, wherein the sequencing system implements a sequencing-by-synthesis method to determine the first subsequence.

18. A method for sequencing polynucleotides, comprising:

receiving a first nucleotide subsequence of a read from a sequencing system during a sequencing run; and

performing a secondary analysis of the first nucleotide subsequence of the read based on a reference sequence using a first analysis path or a second analysis path, wherein the second analysis path is more computationally efficient than the first processing path in performing the secondary analysis.

19. The method of claim 18, wherein performing the secondary analysis comprises processing the first nucleotide subsequence to determine a first plurality of candidate locations of the read that align to the reference sequence using:

a first alignment path if the read is not aligned to the reference sequence is the previously iteration,

a second alignment path if otherwise,

wherein the second alignment path is more computationally efficient than the first alignment path to determine the first plurality of candidate locations of the read.

20. The method of claim 19, wherein processing the second nucleotide subsequence using the second alignment path comprises performing a simple alignment to determine a simple alignment score.

21. The method of claim 19, wherein results of the secondary analysis comprises output of the first alignment path, output of the second alignment path, or any combination thereof.

22. The method of claim 18, wherein performing the secondary analysis comprises performing variant calling of the first nucleotide subsequence comprises:

performing variant calling on the output of a first or a second alignment path using a first variant calling path or a second variant calling path, wherein the second variant calling path is more computationally efficient than the first variant calling path in variant calling of the first subsequence.

23. The method of claim 22, wherein results of the secondary analysis comprises output of the first variant calling path, output of the second variant calling path, or any combination thereof.

24. The method of claim 18, further comprising providing a user with results of the secondary analysis during the sequencing run.

25. The method of claim 24, wherein the results of the secondary analysis are provided to the user at fixed intervals.

26. The method of claim 24, wherein the results of the secondary analysis are provided to the user at request of the user.

27. The method of claim 18, wherein performing the secondary analysis comprises performing the secondary analysis of the first nucleotide subsequence of the read based on results from a prior sequencing interval of the sequencing run.