Abstract: Method and apparatus for the coding and selective access of compressed genomic sequence data produced by genomic sequencing machines. The coding process is based on aligning sequence reads with respect to pre-existing or constructed reference sequences, on classifying and coding the sequence reads by means of sets of descriptors, and further partitioning the descriptor sets into access units of different types. Efficient selective access to specific genomic regions with the guarantee of retrieving all sequence reads mapped to those regions, is provided by: signaling the type of data mapping configuration used to store or transmit the descriptor sets, determining the minimum number of access units that need to be retrieved and decoded to access a genomic region, providing a master index table that contain all information for optimizing the data access process.

Abstract: Method and apparatus for the indexing of genome sequence data produced by genome sequencing machines. The proposed method can be applied both to raw sequence data produced by sequencing machines and to those sequence reads that cannot be mapped on any reference sequence according to specific matching criteria. This invention describes a method to partition and index unaligned sequence reads to enable browsing and efficient selective access.

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.

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.

Abstract: The storage or transmission of genomic data is realized by employing a structured compressed genomic dataset in a file or in a stream of genomic data. Selective access to the data, or subsets of the data, corresponding to specific genomic regions is achieved by employing user-defined labels based on data classification and a specific indexing mechanism.

Abstract: Method and apparatus for the coding and selective access of compressed genomic sequence data produced by genomic sequencing machines. The coding process is based on aligning sequence reads with respect to pre-existing or constructed reference sequences, on classifying and coding the sequence reads by means of sets of descriptors, and further partitioning the descriptor sets into access units of different types. Efficient selective access to specific genomic regions with the guarantee of retrieving all sequence reads mapped to those regions, is provided by: signaling the type of data mapping configuration used to store or transmit the descriptor sets, determining the minimum number of access units that need to be retrieved and decoded to access a genomic region, providing a master index table that contain all information for optimizing the data access process.

Abstract: Method and apparatus for the indexing of genome sequence data produced by genome sequencing machines. The proposed method can be applied both to raw sequence data produced by sequencing machines and to those sequence reads that cannot be mapped on any reference sequence according to specific matching criteria. This invention describes a method to partition and index unaligned sequence reads to enable browsing and efficient selective access.

Abstract: The method and apparatus described in this disclosure include representing a reference genome in terms of syntax elements describing the differences between said reference genome and previously aligned genomic sequences. Each of the aligned genomic sequence is described by means of a subset of syntax elements. Syntax elements describing all the genomic sequences are partitioned in blocks according to their statistical properties. Each block of syntax elements is entropy coded. The entropy coded blocks are then concatenated to form a compressed bitstream. The differences between the reference genome and the aligned sequences are expressed in terms of syntax elements, which are embedded in the bitstream of coded blocks of syntax elements describing aligned reads. The disclosed method enables the reconstruction of the reference genome used for alignment when decoding the compressed genomic sequences while preserving different options of random access on the compressed data and enabling efficient compression.

Abstract: Method and apparatus for the representation and processing of genome sequence data, produced by genome sequencing machines, when aligned on one or more reference sequences. Sequence reads are coded by aligning them with respect to pre-existing or constructed reference sequences. After the alignment, the coding process is composed of a classification of the reads into data classes, followed by the coding of each data class in terms of a multiplicity of descriptors layers. Specific source models and entropy coders are used for the coding of the sub-sets of descriptors used to represent each data class.