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 system for storing and accessing genomic data. Genomic sequencing data are partitioned into access units of different types based on the predictability of the contained data. Access units are classified in different types and the structuring enables selective access and selective processing of genomic data.

Abstract: Method and apparatus for the representation of genome sequence data organized in a structured file format. The data structure contains the representation of nucleotide sequences: in compressed form, aligned and referenced to one or more reference sequences and classified according to different degrees of matching accuracy. The classified and aligned reads are coded in the form of layers of syntax elements, which including a header information are partitioned into independent or dependent access units.

Abstract: Method and system for storing and accessing genomic data. Genomic sequencing data are partitioned into access units of different types based on the predictability of the contained data. Access units are classified in different types and the structuring enables selective access and selective processing of genomic data.

Abstract: Method and system for the transmission of genomic data. The transmission of genomic data is realized by employing the multiplexing of a structured compressed genomic dataset in a stream of genomic data partitioned into randomly accessible access units.

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: Method and apparatus for the compression of genome sequence data produced by genome sequencing machines. The sequences of nucleotides are aligned to one or more reference sequences, classified according to matching accuracy degrees, coded as a multiplicity of layers of syntax elements, using different source models and entropy coders for each layer in which the data is partitioned.

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: 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.