Method and systems for the efficient compression of genomic sequence reads
AssigneeGenomsys SA
InventorsClaudio ALBERTI, Mohamed Khoso BALUCH
Life of this patent
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Abstract
Method and apparatus for the compression of genome sequence data produced by genome sequencing machines. Sequence reads are coded by aligning them with respect to pre-existing or constructed reference sequences, the coding process is composed of a classification of the reads into data classes followed by the coding of each class in terms of a multiplicity of genomic descriptors. Genomic descriptors of the same type are organized in blocks which are compressed by applying successive transformation stages, binarization and entropy coding. Specific source models and entropy coders are used for each data class and for each associated descriptor.
Claims82
A method for encoding genome sequence data, said genome sequence data comprising reads of sequences of nucleotides, said method comprising the steps of:
- aligning said reads to one or more reference sequences thereby creating aligned reads, classifying said aligned reads according to specified matching rules with said one or more reference sequences, thereby creating classes of aligned reads, represented by genomic descriptors arranged in blocks of homogeneous data,
- encoding said classified aligned reads as a multiplicity of blocks of syntax elements, and structuring said blocks of syntax elements and said descriptors with header information thereby creating successive Access Units,
- wherein said encoding further comprises binarizing and entropy coding said genomic descriptors.
A method for decoding encoded genomic data, wherein said genome sequence data comprising reads of sequences of nucleotides, said method comprising the steps of:
- parsing Access Units containing said encoded genomic data to extract multiple blocks of genomic descriptors by employing header information;
- and
- decoding said multiplicity of blocks;
- wherein said decoding of multiplicity of blocks comprise decoding and de-binarizing genomic descriptors arranged in blocks of homogeneous data to extract aligned reads according to specific matching rules defining their classification with respect to one or more reference sequences.
Dependencies are inferred from the claim text.