IP Library › Granted Patent US 12,640,233
Granted Patent B2
US 12,640,233 · App. 18/540,814 · Granted May 26, 2026

Method for the compression of genome sequence data

Inventor: Guillaume Alexandre Pascal Rizk (Rennes, FR)
Assignee: Illumina, Inc.
G16B30/10G06F16/2365G16B20/20G16B30/20G16B45/00G16B50/50
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Quick Facts
Patent No.
US 12,640,233
App. No.
18/540,814
Granted
May 26, 2026
Kind
B2
Abstract

Systems, methods, computer programs, and hardware circuits for compressing genomic sequence data. In one aspect, the method can include obtaining a read record, determining whether the read record corresponds to a read that is perfectly mapped to a reference sequence or imperfectly mapped to the reference sequence, based on determining that the read record corresponds to a read that is imperfectly mapped to the reference sequence whether a number of mismatches of the imperfectly mapped read does not exceed a predetermined threshold number of mismatches, and based on determining that the number of mismatches does not exceed the predetermined threshold number of mismatches, (i) obtaining an offset from a previous mismatch that is lower than a maximum encodable offset value and (ii) encoding each mismatch of the imperfectly mapped read and the offset from the previous mismatch of the read into a record having a size of 1 byte.

Claims (99)

1 . A method for compressing genomic sequence data, the method comprising:

obtaining, by one or more computers, a read record;

determining, by the one or more computers, that the read record corresponds to a read that is imperfectly mapped to the reference sequence;

determining, by the one or more computers, that a number of mismatches of the imperfectly mapped read does not exceed a predetermined threshold number of mismatches;

obtaining, by the one or more computers, an offset from a previous mismatch that is lower than a maximum encodable offset value, wherein the maximum encodable offset value corresponds to a size of a portion of a field of a compressed read record that is to be allocated for storing the obtained offset; and

encoding, by the one or more computers, each mismatch of the imperfectly mapped read and the offset from the previous mismatch of the read into a compressed read record having a size of 1 byte.

2 . The method of claim 1 , wherein the method further comprises:

obtaining, by the one or more computers, an additional read record;

determining, by the one or more computers, that the additional read record corresponds to an additional read that is imperfectly mapped to the reference sequence;

determining, by the one or more computers, that a number of mismatches of the imperfectly mapped additional read exceeds the predetermined threshold number of mismatches; and

encoding, by the one or more computers, each base of the imperfectly mapped additional read individually in a compressed read record for the additional read.

3 . The method of claim 1 , wherein each read record comprises:

data indicating an absolute starting position of an aligned read with respect to the reference sequence;

data indicating a length of the read;

data indicating whether the read is perfectly mapped or imperfectly mapped;

data indicating a number of mismatches identified in the read; and

data indicating a relative position of each of said mismatches in the read.

4 . The method of claim 1 , wherein encoding each mismatch of the imperfectly mapped read into a compressed read record having a size of 1 byte comprises, for each particular mismatch:

encoding, by the one or more computers, a first two bits of the byte to include data representing an alternate nucleotide or base present in the read instead of a corresponding reference nucleotide or base in the reference sequence; and

encoding, by one or more computers, six remaining bits of the byte to include data representing the offset.

5 . The method of claim 4 , the method further comprising:

determining, by one or more computers, that the offset is greater than a maximum encodable value; and

inserting, by one or more computers, at least one fake mismatch between the particular mismatch and the previous mismatch.

6 . The method of claim 1 , the method further comprising:

obtaining, by the one or more computers, an additional read record;

determining, by the one or more computers, that the additional read record corresponds to an additional read that is perfectly mapped to the reference sequence;

encoding, by one or more computers, at least a portion of the additional read record into a compressed read record for the additional read using reduced information entropy encoding.

7 . A hardware processor that includes hardware processing circuitry that is configured to perform one or more operations, the one or more operations comprising:

obtaining, by the hardware processing circuitry, a read record;

determining, by the hardware processing circuitry, whether the read record corresponds to a read that is perfectly mapped to a reference sequence or imperfectly mapped to the reference sequence;

based on determining, by the hardware processing circuitry, that the read record corresponds to a read that is imperfectly mapped to the reference sequence, determining, by the one or more computers, whether a number of mismatches of the imperfectly mapped read does not exceed a predetermined threshold number of mismatches; and

based on determining that the number of mismatches does not exceed the predetermined threshold number of mismatches, (i) obtaining, by the hardware processing circuitry, an offset from a previous mismatch that is lower than a maximum encodable offset value, wherein the maximum encodable offset value corresponds to a size of a portion of a field of a compressed read record that is to be allocated for storing the obtained offset and (ii) encoding, by the hardware processing circuitry, each mismatch of the imperfectly mapped read and the offset from the previous mismatch of the read into a compressed read record having a size of 1 byte.

8 . The hardware processor of claim 7 , wherein each read record comprises:

data indicating an absolute starting position of the aligned read with respect to the reference sequence;

data indicating a length of the read;

data indicating whether the read is perfectly mapped or imperfectly mapped;

data indicating a number of mismatches identified in the read; and

data indicating a relative position of said mismatches in the read.

9 . The hardware processor of claim 7 , wherein encoding each mismatch of the imperfectly mapped read into a compressed read record having a size of 1 byte comprises for each particular mismatch:

encoding, by the hardware processing circuitry, a first two bits of the byte to include data representing an alternate nucleotide or base present in the read instead of a corresponding reference nucleotide or base in the reference sequence; and

encoding, by the hardware processing circuitry, a six remaining bits of the byte to include data representing the offset.

10 . The hardware processor of claim 9 , wherein the hardware processor circuitry is further configured to perform operations comprising:

determining, by the hardware processing circuitry, whether the offset is greater than a maximum encodable value;

based on determining that the offset is greater than the maximum encodable value, inserting, by the hardware processing circuitry, at least one fake mismatch between the particular mismatch and the previous mismatch.

11 . The hardware processor of claim 7 , wherein the hardware processor circuitry is further configured to perform operations comprising:

based on determining that the read record corresponds to a read that is perfectly mapped to the reference sequence, encoding, by the hardware processing circuitry, at least a portion of the read record using reduced information entropy encoding.

12 . The hardware processor of claim 7 wherein the hardware processing circuitry comprises one or more field programmable gate arrays (FPGAs).

13 . The hardware processor of claim 7 , wherein the one or more operations further comprise:

determining, by the hardware processing circuitry, that the number of mismatches of the imperfectly mapped read exceeds the predetermined threshold number of mismatches; and

based on determining that that the number of mismatches of the imperfectly mapped read exceeds the predetermined threshold number of mismatches, encoding each base of the imperfectly mapped read individually.

14 . A system for compressing genomic sequence data, the system comprising:

one or more computers and one or more storage devices storing instructions that are operable, when executed by one or more computers, to cause the one or more computers to perform the operations comprising:

obtaining, by the one or more computers, a read record;

determining, by the one or more computers, whether the read record corresponds to a read that is perfectly mapped to a reference sequence or imperfectly mapped to the reference sequence;

based on determining, by the one or more computers, that the read record corresponds to a read that is imperfectly mapped to the reference sequence, determining, by the one or more computers, whether a number of mismatches of the imperfectly mapped read does not exceed a predetermined threshold number of mismatches; and

based on determining that the number of mismatches does not exceed the predetermined threshold number of mismatches, (i) obtaining, by the one or more computers, an offset from a previous mismatch that is lower than a maximum encodable offset value and (ii) encoding, by the one or more computers, each mismatch of the imperfectly mapped read and the offset from the previous mismatch of the read into a record having a size of 1 byte.

15 . The system of claim 14 , wherein each read record comprises:

data indicating an absolute starting position of an aligned read with respect to the reference sequence;

data indicating a length of the read;

data indicating whether the read is perfectly mapped or imperfectly mapped;

data indicating a number of mismatches identified in the read; and

data indicating a relative position of each of said mismatches in the read.

16 . The system of claim 14 , wherein encoding each mismatch of the imperfectly mapped read into a record having a size of 1 byte comprises, for each particular mismatch:

encoding, by one or more computers, a first two bits of the byte to include data representing an alternate nucleotide or base present in the read instead of a corresponding reference nucleotide or base in the reference sequence; and

encoding, by one or more computers, six remaining bits of the byte to include data representing the offset.

17 . The system of claim 16 , the operations further comprising:

determining, by the one or more computers, whether the offset is greater than a maximum encodable value; and

based on determining that the offset is greater than the maximum encodable value, inserting, by one or more computers, at least one fake mismatch between the particular mismatch and the previous mismatch.

18 . The system of claim 14 , the operations further comprising:

based on determining that the read record corresponds to a read that is perfectly mapped to the reference sequence, encoding, by one or more computers, at least a portion of the read record using reduced information entropy encoding.

19 . The system of claim 14 , wherein the one or more computers comprises one or more hardware processors.

20 . The system of claim 19 wherein the one or more hardware processors comprises one or more field programmable gate arrays (FPGAs).

21 . The system of claim 14 , wherein the operations further comprise:

determining, by the hardware processing circuitry, that the number of mismatches of the imperfectly mapped read exceeds the predetermined threshold number of mismatches; and

based on determining that that the number of mismatches of the imperfectly mapped read exceeds the predetermined threshold number of mismatches, encoding each base of the imperfectly mapped read individually in a compressed read record.

22 . A non-transitory computer-readable storage device having stored thereon instructions, which, when executed by a data processing apparatus, cause the data processing apparatus to perform operations for compressing genomic sequence data, the operations comprising:

obtaining a read record;

determining whether the read record corresponds to a read that is perfectly mapped to a reference sequence or imperfectly mapped to the reference sequence;

based on determining that the read record corresponds to a read that is imperfectly mapped to the reference sequence, determining whether a number of mismatches of the imperfectly mapped read does not exceed a predetermined threshold number of mismatches; and

based on determining that the number of mismatches does not exceed the predetermined threshold number of mismatches, (i) obtaining an offset from a previous mismatch that is lower than a maximum encodable offset value, wherein the maximum encodable offset value corresponds to a size of a portion of a field of a compressed read record that is to be allocated for storing the obtained offset and (ii) encoding each mismatch of the imperfectly mapped read and the offset from the previous mismatch of the read into a compressed read record having a size of 1 byte.

23 . The non-transitory computer-readable storage device of claim 22 , wherein each read record comprises:

data indicating an absolute starting position of an aligned read with respect to the reference sequence;

data indicating a length of the read;

data indicating whether the read is perfectly mapped or imperfectly mapped;

data indicating a number of mismatches identified in the read; and

data indicating a relative position of each of said mismatches in the read.

24 . The non-transitory computer-readable storage device of claim 22 , wherein encoding each mismatch of the imperfectly mapped read into a compressed read record having a size of 1 byte comprises, for each particular mismatch:

encoding, by one or more computers, a first two bits of the byte to include data representing an alternate nucleotide or base present in the read instead of a corresponding reference nucleotide or base in the reference sequence; and

encoding, by one or more computers, six remaining bits of the byte to include data representing the offset.

25 . The non-transitory computer-readable storage device of claim 24 , the operations further comprising:

determining, by the one or more computers, whether the offset is greater than a maximum encodable value; and

based on determining that the offset is greater than the maximum encodable value, inserting, by one or more computers, at least one fake mismatch between the particular mismatch and the previous mismatch.

26 . The non-transitory computer-readable storage device of claim 22 , the operations further comprising:

based on determining that the number of mismatches does not satisfy the predetermined threshold number of mismatches, encoding a list of positions of the reference sequence corresponding to a position of each of the mismatches to the reference sequence using a reduced information entropy encoding process.

27 . The non-transitory computer-readable storage device of claim 22 , the operations further comprising:

based on determining that the read record corresponds to a read that is perfectly mapped to the reference sequence, encoding at least a portion of the read record into a compressed read record using reduced information entropy encoding.

28 . The non-transitory computer-readable storage device of claim 22 , wherein the operations further comprise:

determining, by the hardware processing circuitry, that the number of mismatches of the imperfectly mapped read exceeds the predetermined threshold number of mismatches; and

based on determining that that the number of mismatches of the imperfectly mapped read exceeds the predetermined threshold number of mismatches, encoding each base of the imperfectly mapped read individually in a compressed read record.

Assignments (2)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Nov 11, 2024
From: RIZK, GUILLAUME
To: ENANCIO
Reel/Frame 069198/0659 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Nov 11, 2024
From: ENANCIO
To: ILLUMINA, INC.
Reel/Frame 069198/0711 →
Continuity (2)
Continuation 16567211 · Sep 11, 2019
Related Publication 20240194296A1 · Jun 13, 2024
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