Quality score compression
AssigneeIllumina, Inc.
InventorGuillaume Alexandre Pascal Rizk
Life of this patent
Estimating the term…
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 method comprising:
- obtaining an encoded data set generated by encoding a read sequence comprising data that corresponds to a plurality of base calls generated by a nucleic acid sequencing device, wherein encoding uses a value representing a number of different quality scores, wherein each quality score indicates a likelihood that a particular base call of the read sequence was correctly generated by the nucleic acid sequencing device;
- generating a decoded data set using the value representing the number of different quality scores;
- ordering the decoded data set within one or more other decoded data sets;
- and
- generating an aggregate decoded data set based on the decoded data set and the one or more other decoded data sets.
One or more non-transitory computer-readable storage media encoded with instructions that, when executed by one or more computers, cause the one or more computers to perform operations comprising:
- obtaining an encoded data set generated by encoding a read sequence comprising data that corresponds to a plurality of base calls generated by a nucleic acid sequencing device, wherein encoding uses a value representing a number of different quality scores, wherein each quality score indicates a likelihood that a particular base call of the read sequence was correctly generated by the nucleic acid sequencing device;
- generating a decoded data set using the value representing the number of different quality scores;
- ordering the decoded data set within one or more other decoded data sets;
- and
- generating an aggregate decoded data set based on the decoded data set and the one or more other decoded data sets.
A system comprising:
- one or more computers and one or more storage devices on which are stored instructions that are operable, when executed by the one or more computers, to cause the one or more computers to perform operations comprising:
- obtaining an encoded data set generated by encoding a read sequence comprising data that corresponds to a plurality of base calls generated by a nucleic acid sequencing device, wherein encoding uses a value representing a number of different quality scores, wherein each quality score indicates a likelihood that a particular base call of the read sequence was correctly generated by the nucleic acid sequencing device;
- generating a decoded data set using the value representing the number of different quality scores;
- ordering the decoded data set within one or more other decoded data sets;
- and
- generating an aggregate decoded data set based on the decoded data set and the one or more other decoded data sets.
Dependencies are inferred from the claim text.