Method for the Compression of Genome Sequence Data

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, 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 satisfies a predetermined threshold number of mismatches;
• and
• based on determining that the number of mismatches satisfies 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.

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 satisfies a predetermined threshold number of mismatches;
• and
• based on determining that the number of mismatches satisfies 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 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 record having a size of 1 byte.

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 satisfies a predetermined threshold number of mismatches;
• and
• based on determining that the number of mismatches satisfies 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.

A 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 satisfies a predetermined threshold number of mismatches;
• and
• based on determining that the number of mismatches satisfies 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.