Method and apparatus for the compact representation of bioinformatics data using multiple genomic descriptors
AssigneeGenomsys SA
InventorsClaudio ALBERTI, Giorgio ZOIA, Daniele RENZI, Mohamed Khoso BALUCH
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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 descriptors blocks. Specific source models and entropy coders are used for each data class in which the data is partitioned, and each associated descriptor block.
Claims66
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,
- encoding said classified aligned reads as a multiplicity of blocks of descriptors,
- wherein encoding said classified aligned reads as a multiplicity of blocks of descriptors comprises selecting said descriptors according to said classes of aligned reads,
- structuring said blocks of descriptors with header information thereby creating successive Access Units.
The method of claim 11 where each Class of reads N, M, I is further partitioned into two or more subclasses (296, 297, 298) according to a vector of thresholds (292, 293, 294) defined respectively for each class N, M and I, by the number of “n type” mismatches (292), the function f(n,s) (293) and the function w(n,s,i,d,c) (294).
A method for decoding encoded genomic data comprising the steps of:
- parsing Access Units containing said encoded genomic data to extract multiple blocks of descriptors by employing header information,
- decoding said multiplicity of blocks of descriptors to extract reads according to specific matching rules defining their classification with respect to one or more reference sequences.
A genomic encoder (2010) for the compression of genome sequence data 209, said genome sequence data 209 comprising reads of sequences of nucleotides,
- said genomic encoder (2010) comprising:
- an aligner unit (201), configured to align said reads to one or more reference sequences thereby creating aligned reads,
- a constructed-reference generator unit (202), configured to produce constructed reference sequences
- a data classification unit (204), configured to classify said aligned reads according to specified matching rules with the one or more pre-existing reference sequences or constructed reference sequences thereby creating classes of aligned reads (208);
- one or more blocks encoding units (205-207), configured to encode said classified aligned reads as blocks of descriptors by selecting said descriptors according to said classes of aligned reads,
- a multiplexer (2016) for multiplexing the compressed genomic data and metadata.
A genomic decoder (218) for the decompression of a compressed genomic stream (211) said genomic decoder (218) comprising:
- a demultiplexer (210) for demultiplexing compressed genomic data and metadata,
- parsing means (212-214) configured to parse said compressed genomic stream into genomic blocks of descriptors (215),
- one or more block decoders (216-217), configured to decode the genomic blocks of descriptors into classified reads of sequences of nucleotides (2111),
- genomic data classes decoders (219) configured to selectively decode said classified reads of sequences, of nucleotides on one or more reference sequences so as to produce uncompressed reads of sequences of nucleotides.
Dependencies are inferred from the claim text.