US 9,817,866 B1Granted

Lossless compression of client read data

AssigneeColor Genomics, Inc.

InventorsRyan Barrett, Othman Laraki

Life of this patent

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Abstract

A read is aligned to a reference data set. It is determined whether the read includes any identifier distinction, the determination being performed using the alignment. If so, positional data corresponding to the identifier distinction(s) are defined. Compressed read data is stored in association with a read identifier of the read. The compressed read data includes alignment information (e.g., a start and/or stop position of the alignment). When the read includes an identifier distinction, the compressed read data further includes the positional data and deviation data characterizing the distinction.

Claims20

Dependent claims

A system for compressing read data based on positional and discrepancy assessments, the system comprising:

one or more data processors;
and
a non-transitory computer readable storage medium containing instructions which when executed on the one or more data processors, cause the one or more data processors to perform actions including:
accessing a first data set that includes a set of reads, each read of the set of reads corresponding to a client and including a set of consecutive identifiers;
for each read of the set of reads:
aligning the read with a portion of a reference data set, the aligning identifying at least one of a start position and a stop position of the read relative to the reference data set;
detecting whether the read includes at least one identifier distinction, each identifier distinction of the at least one identifier distinction representing a distinction between one or more identifiers of the set of consecutive identifiers in the read relative to one or more corresponding identifiers in the reference data set, wherein the one or more identifiers of the set of consecutive identifiers having been aligned to one or more positions associated with the one or more corresponding identifiers in the reference data set;
defining, for each identifier distinction of the at least one identifier distinction, positional data representing the one or more positions;
and
storing, in a data store and in association with a respective read identifier of the set of consecutive identifiers in the read, compressed read data that includes:
the at least one of the start position and the stop position;
and
when the at least one identifier distinction is detected:
the positional data for each identifier distinction detected for the read;
and
deviation data that characterizes a distinction between the one or more identifiers relative to the one or more corresponding identifiers;
wherein, for each identifier of the set of consecutive identifiers in the read that is not represented at least in part by the at least one identifier distinction, the identifier is omitted from the compressed read data.

14 more elements

A method for compressing read data based on positional and discrepancy assessments, the method comprising:

accessing a first data set that includes a set of reads, each read of the set of reads corresponding to a client and including a set of consecutive identifiers;
for each read of the set of reads and using one or more data processors:
aligning the read with a portion of a reference data set, the aligning identifying at least one of a start position and a stop position of the read relative to the reference data set;
detecting whether the read includes at least one identifier distinction, each identifier distinction of the at least one identifier distinction representing a distinction between one or more identifiers of the set of consecutive identifiers in the read relative to one or more corresponding identifiers in the reference data set, wherein the one or more identifiers of the set of consecutive identifiers having been aligned to one or more positions associated with the one or more corresponding identifiers in the reference data set;
defining, for each identifier distinction of the at least one identifier distinction, positional data representing the one or more positions;
and
storing, in a data store and in association with a respective read identifier of the set of consecutive identifiers in the read, compressed read data that includes:
the at least one of the start position and the stop position;
and
when the at least one identifier distinction is detected:
the positional data for each identifier distinction detected for the read;
and
deviation data that characterizes a distinction between the one or more identifiers relative to the one or more corresponding identifiers;
wherein, for each identifier of the set of consecutive identifiers in the read that is not represented at least in part by the at least one identifier distinction, the identifier is omitted from the compressed read data.

11 more elements

A computer-program product tangibly embodied in a non-transitory machine-readable storage medium, including instructions configured to cause one or more data processors to perform actions including:

accessing a first data set that includes a set of reads, each read of the set of reads corresponding to a client and including a set of consecutive identifiers;
for each read of the set of reads:
aligning the read with a portion of a reference data set, the aligning identifying at least one of a start position and a stop position of the read relative to the reference data set;
detecting whether the read includes at least one identifier distinction, each identifier distinction of the at least one identifier distinction representing a distinction between one or more identifiers of the set of consecutive identifiers in the read relative to one or more corresponding identifiers in the reference data, wherein the one or more identifiers of the set of consecutive identifiers having been aligned to one or more positions associated with the one or more corresponding identifiers in the reference data set;
defining, for each identifier distinction of the at least one identifier distinction, positional data representing the one or more positions;
and
storing, in a data store and in association with a respective read identifier of the set of consecutive identifiers in the read, compressed read data that includes:
the at least one of the start and stop position;
and
when the at least one identifier distinction is detected:
the positional data for each identifier distinction detected for the read;
and
deviation data that characterizes a distinction between the one or more identifiers relative to the one or more corresponding identifiers;
wherein, for each identifier of the set of consecutive identifiers in the read that is not represented at least in part by the at least one identifier distinction, the identifier is omitted from the compressed read data.

11 more elements

Dependencies are inferred from the claim text.

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Abstract

A system for compressing read data based on positional and discrepancy assessments, the system comprising:

one or more data processors;
and
a non-transitory computer readable storage medium containing instructions which when executed on the one or more data processors, cause the one or more data processors to perform actions including:
accessing a first data set that includes a set of reads, each read of the set of reads corresponding to a client and including a set of consecutive identifiers;
for each read of the set of reads:
aligning the read with a portion of a reference data set, the aligning identifying at least one of a start position and a stop position of the read relative to the reference data set;
detecting whether the read includes at least one identifier distinction, each identifier distinction of the at least one identifier distinction representing a distinction between one or more identifiers of the set of consecutive identifiers in the read relative to one or more corresponding identifiers in the reference data set, wherein the one or more identifiers of the set of consecutive identifiers having been aligned to one or more positions associated with the one or more corresponding identifiers in the reference data set;
defining, for each identifier distinction of the at least one identifier distinction, positional data representing the one or more positions;
and
storing, in a data store and in association with a respective read identifier of the set of consecutive identifiers in the read, compressed read data that includes:
the at least one of the start position and the stop position;
and
when the at least one identifier distinction is detected:
the positional data for each identifier distinction detected for the read;
and
deviation data that characterizes a distinction between the one or more identifiers relative to the one or more corresponding identifiers;
wherein, for each identifier of the set of consecutive identifiers in the read that is not represented at least in part by the at least one identifier distinction, the identifier is omitted from the compressed read data.

14 more elements