Improved Quality Value Compression Framework in Aligned Sequencing Data Based on Novel Contexts
AssigneeKoninklijke Philips N.V.
InventorsShubham Chandak, Yee Him Cheung
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Abstract
A method for compressing information includes accessing a read of genomic sequencing data, aligning the read to a reference, generating alignment data based on alignment of the read, obtaining a set of contexts based on the alignment data, and compressing quality values corresponding to the alignment data based on the set of contexts. The alignment data may provide an indication of errors in the genomic sequencing data, and each of the quality values may provide an indication of a probability of error at one or more bases in the genomic sequencing data.
Claims22
A method for compressing genomic information, comprising:
- (a) accessing a read of genomic sequencing data;
- (b) aligning the read to a reference;
- (c) generating alignment data, which comprises an alignment position on the reference and a characterization of matches and mismatches of bases in the read compared to bases in the reference at alignment position, such as a CIGAR representation, after alignment of the read;
- (d) arithmetically compressing quality values of the read, wherein each of the quality values provides an indication of a Probability of error of a base in the genomic sequencing data, wherein the compressing comprises:
- (e) selecting a set of one or more arithmetic compression contexts, characterized in that at least one of the arithmetic compression contexts is based on the alignment data, wherein such at least one of the arithmetic compression contexts based on the alignment data comprises selecting from:
- whether the base in the read at the position of the quality value matches the base in the reference;
- the type of mismatch at the position of the quality value, being an insertion, deletion or substitution,
- the type of bases in the reference surrounding the position on the reference corresponding to the position of the quality value in the read, and
- a mean quality value of bases surrounding the position on the the reference corresponding to the position of the quality value in the read.
A system for compressing information, comprising:
- a memory configured to store instructions;
- and
- a processor configured to execute the instructions to:
- (a) access a read of genomic sequencing data;
- (b) align the read to a reference;
- (c) generate alignment data based on alignment of the read, which comprises an alignment position on the reference and a characterization of matches and mismatches of bases in the read compared to bases in the reference at alignment position, such as a CIGAR representation;
- (d) obtain a sequence of quality values for the read, wherein each of the quality values provides an indication of a probability of error of a base in the genomic sequencing data,
- (e) select a set of one or more arithmetic encoding contexts, characterized in that these one or more arithmetic encoding contexts are based on the alignment data, wherein such at least one of the arithmetic compression contexts based on the alignment data comprises is selected from:
- whether the base in the read at the position of the quality value matches the base in the reference;
- the type of mismatch at the position of the quality value, being an insertion, deletion or substitution,
- the type of bases in the reference surrounding the position on the reference corresponding to the position of the quality value in the read, and
- a mean quality value of bases surrounding the position on the the reference corresponding to the position of the quality value in the read;
- and;
- (f) arithmetically compress the quality values using the set of contexts.
Dependencies are inferred from the claim text.