US 12,404,548 B2
Incremental secondary analysis of nucleic acid sequences
Michael J. Carney, San Diego, CA (US); Jacobus De Beer, San Diego, CA (US); Hsu-Lin Tsao, San Diego, CA (US); Partha Mukherjee, San Diego, CA (US); and Daniel Joseph Tracy, San Diego, CA (US)
Assigned to ILLUMINA, INC., San Diego, CA (US)
Filed by Illumina, Inc., San Diego, CA (US)
Filed on Mar. 11, 2021, as Appl. No. 17/199,391.
Claims priority of provisional application 62/988,374, filed on Mar. 11, 2020.
Prior Publication US 2021/0285043 A1, Sep. 16, 2021
Int. Cl. C12Q 1/6869 (2018.01); G06N 3/12 (2023.01); G16B 20/20 (2019.01); G16B 30/10 (2019.01)
CPC C12Q 1/6869 (2013.01) [G06N 3/12 (2013.01); G16B 20/20 (2019.02); G16B 30/10 (2019.02)] 35 Claims
 
1. A method for performing incremental secondary analysis of nucleic acid sequence reads, the method comprising:
(i) obtaining, by one or more processors of a nucleic acid sequencing device, first data describing a plurality of first reads generated by the nucleic acid sequencing device during a first read interval, wherein each read of the first reads represents a first ordered sequence of nucleotides
(ii) obtaining, by one or more processors of the nucleic acid sequencing device, second data describing a plurality of second reads generated by the nucleic acid sequencing device during a second read interval that is performed after the first read interval, wherein each read of the second reads represents a second ordered sequence of nucleotides, wherein while the second data is being obtained, the method further comprises:
(a) providing, by one or more processors of the nucleic acid sequencing device, the first data as an input to a mapping and alignment engine;
(b) receiving, by one or more processors of the nucleic acid sequencing device and from the mapping and alignment engine alignment results that indicate a quality of an alignment of the first data;
(c) determining, by one or more processors of the nucleic acid sequencing device and based on the received alignment results of the first data, that the nucleic acid sequencing device is to terminate operations that obtain the second data; and
(d) causing, by one or more processors of the nucleic acid sequencing device, the nucleic acid sequencing device to terminate operations that obtain the second data.