Quality score compression
AssigneeIllumina, Inc.
InventorGuillaume Alexandre Pascal Rizk
Life of this patent
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Abstract
Methods, systems, and computer programs for compressing nucleic acid sequence data. A method can include obtaining nucleic acid sequence data representing: (i) a read sequence, and (ii) a plurality of quality scores, determining whether the read sequence includes at least one “N” base, based on a determination that the read sequence includes at least one “N” base, generating, by one or more computers, a first encoding data set by using a first encoding process to encode each set of four quality scores of the read sequence into a single byte of memory, and using a second encoding process to encode the first encoded data set, thereby compressing the data to be compressed.
Claims20
A system for compressing nucleic acid sequence data, the system comprising:
- one or more data processing apparatus;
- and
- one or more non-transitory computer-readable storage devices having stored thereon instructions that, when executed by the one or more data processing apparatus, cause the one or more data processing apparatus to perform operations, the operations comprising:
- obtaining nucleic acid sequence data representing:
- (i) a read sequence comprising data that corresponds to a plurality of base calls generated by a nucleic acid sequencing device, and
- (ii) a plurality of quality scores, wherein each quality score of the plurality of quality scores indicates a likelihood that a particular base call of the read sequence was correctly generated by a nucleic acid sequencing device;
- determining whether the read sequence includes at least one “N” base;
- based on a determination that the read sequence includes at least one “N” base, generating a first encoding data set by using a first encoding process to encode each set of four quality scores of the read sequence into a single byte of memory;
- and
- using a second encoding process to encode the first encoding data set.
A method for compressing nucleic acid sequence data, the method comprising:
- obtaining, by one or more computers, nucleic acid sequence data representing:
- (i) a read sequence comprising data that corresponds to a plurality of base calls generated by a nucleic acid sequencing device, and
- (ii) a plurality of quality scores, wherein each quality score of the plurality of quality scores indicates a likelihood that a particular base call of the read sequence was correctly generated by a nucleic acid sequencing device;
- determining, by one or more computers, whether the read sequence includes at least one “N” base;
- based on a determination that the read sequence includes at least one “N” base, generating, by one or more computers, a first encoding data set by using a first encoding process to encode each set of four quality scores of the read sequence into a single byte of memory;
- and
- using, by one or more computers, a second encoding process to encode the first encoding data set.
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, the operations comprising:
- obtaining nucleic acid sequence data representing:
- (i) a read sequence comprising data that corresponds to a plurality of base calls generated by a nucleic acid sequencing device, and
- (ii) a plurality of quality scores, wherein each quality score of the plurality of quality scores indicates a likelihood that a particular base call of the read sequence was correctly generated by a nucleic acid sequencing device;
- determining whether the read sequence includes at least one “N” base;
- based on a determination that the read sequence includes at least one “N” base, generating a first encoding data set by using a first encoding process to encode each set of four quality scores of the read sequence into a single byte of memory;
- and
- using a second encoding process to encode the first encoding data set.
Dependencies are inferred from the claim text.