Method and system for analyzing sequences

1 . A method performed by one or more processors, the method comprising:

determining a target length for sequence production based on a ratio of tumor cells included in a sample of an organism to non-tumor cells included in the sample;

causing a sequencer to process an amount of the sample corresponding to the target length;

causing the sequencer to perform imaging of the sample by causing the sequencer to capture:

first image data associated with a first polynucleotide chain of a genome of the organism; and

second image data associated with a second polynucleotide chain of the genome;

converting, in real time and during communications with the sequencer during the imaging, the first image data and the second image data into marking code corresponding to identified nucleotides;

converting, in real-time and during the communications with the sequencer during the imaging, the marking code to corresponding sequence data by:

recording the marking codes in marking data that indicates:

a first length of the first polynucleotide chain of the genome of the sample; and

a second length of the second polynucleotide chain of the genome, wherein the second length is shorter than the first length;

converting the marking data to sequence data;

aligning, based on reference sequence data associated with the organism, the sequence data, wherein the aligned sequence data comprises:

a first aligned portion corresponding to a first read of paired-end reads; and

a second aligned portion corresponding to a partial portion of a second read of the paired-end reads, wherein the second read is associated with the second length of the second polynucleotide chain; and

performing, based on the aligned sequence data, a partial genome sequence-based identification process to identify at least one structural variant different from point mutations.

2 . The method according to claim 1 , wherein the amount is based on an amount of data required for early reporting of a variant identification result, and

wherein a size of the converted sequence data corresponds to a size associated with the target length.

3 . The method according to claim 1 , further comprising:

before the aligning the sequence data:

receiving prior marking data from the sequencer, wherein the prior marking data comprises an image data portion associated with a length of the first polynucleotide chain that is shorter than the first length of the first polynucleotide chain;

converting, for a second partial genome sequence-based identification, the prior marking data to prior sequence data;

aligning, based on the reference sequence data, the converted prior sequence data; and

performing, based on the aligned prior sequence data, the second partial genome sequence-based identification to identify at least one point mutation.

4 . The method according to claim 3 , further comprising:

generating a report comprising information on at least one of an identified point mutation or an identified structural variant.

5 . The method according to claim 1 , further comprising:

before the aligning the sequence data,

aligning, based on the reference sequence data, prior sequence data, wherein the prior sequence data is generated based on prior marking data, and wherein the prior marking data comprises an image data portion associated with a length of the first polynucleotide chain that is shorter than the first length of the first polynucleotide chain; and

determining, based on a failure associated with the aligning the prior sequence data, an alignment operation associated with the sequence data.

6 . The method according to claim 5 , wherein the reference sequence data comprises a plurality of sub-regions, and

wherein the method further comprises:

calculating an alignment ratio, wherein the alignment ratio comprises a ratio of deoxyribonucleic acid (DNA) reads uniquely aligned to one sub-region of the plurality of sub-regions to DNA reads included in the prior sequence data; and

based on the calculated alignment ratio being less than a target alignment ratio, determining the failure associated with the aligning the prior sequence data.

7 . The method according to claim 5 , further comprising:

after the determining the failure, retrying an alignment of the prior sequence data,

wherein the retrying the alignment of the prior sequence data is based on:

additional nucleotide identifiers being added to the prior sequence data; and

a number of the additional nucleotide identifiers added to the prior sequence data satisfying a predetermined threshold number.

8 . The method according to claim 7 , further comprising:

before the aligning the prior sequence data,

acquiring target variant information; and

determining, from an entire region associated with the reference sequence data, a sub-region of the reference sequence data, wherein the sub-region is associated with the target variant information, and

wherein the determining the alignment operation associated with the sequence data is based on a determination that the prior sequence data is not mapped to the determined sub-region.

9 . The method according to claim 1 , further comprising:

before the recording the marking codes in the marking data, determining a time for early reporting of a variant identification result; and

based on the determined time, determining the target length.

10 . The method according to claim 9 , wherein the second length satisfies the target length.

11 . The method according to claim 1 , wherein the target length corresponds to at least one structural variant different from point mutations.

12 . The method according to claim 1 , wherein the target length is based on at least one of:

a plurality of cycles of the sequencer; or

a data size of the marking data associated with the sample of the organism.

13 . The method according to claim 1 , further comprising:

identifying, based on a disease type of a test subject, the ratio.

14 . A non-transitory computer-readable medium storing instructions that, when executed, cause:

determining a target length for sequence production based on a ratio of tumor cells included in a sample of an organism to non-tumor cells included in the sample;

causing a sequencer to process an amount of the sample corresponding to the target length;

causing the sequencer to perform imaging of the sample by causing the sequencer to capture:

first image data associated with a first polynucleotide chain of a genome of the organism; and

second image data associated with a second polynucleotide chain of the genome;

converting, in real time and during communications with the sequencer during the imaging, the first image data and the second image data into marking code corresponding to identified nucleotides;

converting, in real time and during communications with the sequencer during the imaging, the marking code to corresponding sequence data by:

recording the marking codes in marking data that indicates:

a first length of the first polynucleotide chain of the genome of the sample; and

a second length of the second polynucleotide chain of the genome, wherein the second length is shorter than the first length;

converting the marking data to sequence data;

aligning, based on reference sequence data associated with the organism, the sequence data, wherein the aligned sequence data comprises:

a first aligned portion corresponding to a first read of paired-end reads; and

a second aligned portion corresponding to a partial portion of a second read of the paired-end reads, wherein the second read is associated with the second length of the second polynucleotide chain; and

performing, based on the aligned sequence data, a partial genome sequence-based identification process to identify at least one structural variant different from point mutations.

15 . The non-transitory computer-readable medium of claim 14 , wherein the amount is based on an amount of data required for early reporting of a variant identification result, and

wherein a size of the converted sequence data corresponds to a size associated with the target length.

16 . The non-transitory computer-readable medium of claim 14 , wherein the instructions, when executed, further cause:

generating a report comprising information on at least one of an identified point mutation or an identified structural variant.

17 . A system comprising:

one or more processors; and

memory storing instructions that, when executed by the one or more processors, cause the system to:

determine a target length for sequence production based on a ratio of tumor cells included in a sample of an organism to non-tumor cells included in the sample;

cause a sequencer to process an amount of the sample corresponding to the target length;

cause the sequencer to perform imaging of the sample by causing the sequencer to capture:

first image data associated with a first polynucleotide chain of a genome of the organism; and

second image data associated with a second polynucleotide chain of the genome;

convert, in real time and during communications with the sequencer during the imaging, the first image data and the second image data into marking code corresponding to identified nucleotides;

convert, in real-time and during communications with the sequencer during the imaging, the marking code to corresponding sequence data by:

recording the marking codes in marking data that indicates:

a first length of the first polynucleotide chain of the genome of the sample; and

a second length of the second polynucleotide chain of the genome, wherein the second length is shorter than the first length;

converting the marking data to sequence data;

align, based on reference sequence data associated with the organism, the sequence data, wherein the aligned sequence data comprises:

a first aligned portion corresponding to a first read of paired-end reads; and

a second aligned portion corresponding to a partial portion of a second read of the paired-end reads, wherein the second read is associated with the second length of the second polynucleotide chain; and

perform, based on the aligned sequence data, a partial genome sequence-based identification process to identify at least one structural variant different from point mutations.