Method and apparatus for the access to bioinformatics data structured in access units

Inventors

Baluch, Mohamed Khoso • Alberti, Claudio • Zoia, Giorgio • Renzi, Daniele

Assignees

Koninklijke Philips NV

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.

Core Innovation

The invention relates to selectively accessing compressed genomic data structured into entropy coded Access Units, where each AU includes genomic records associated with a genomic region. The system uses an indexing table disjointly coded from the Access Units, from which it extracts values of start coordinate s_i and end coordinate e_i for the Access Units, enabling selective access by identifying which AUs cover a queried genomic interval.

The invention additionally extracts a threshold value MaxD from the dataset header of the file, where MaxD specifies the maximum value that the pairing distance of read pairs can assume. This MaxD governs whether read pairs are coded as single entity or separately coded, and the same threshold value MaxD is parsed for decoding.

For efficient selective access and file organization, the invention uses a Master Index Table including AU start and end coordinates and byte offsets to descriptor blocks, along with descriptor stream sizes or AU sizes depending on the selected storage mode. The disclosed file layout supports selective access using modes in which blocks of data for different descriptors of the same AU are stored contiguously, or blocks belonging to the same descriptors across different AUs are stored in contiguous regions.

Claims Coverage

The independent claims cover three core aspects of the disclosed approach: selective access to entropy coded Access Units by parsing AU start and end coordinates from an indexing table, coding and decoding using a dataset-header threshold MaxD that controls coding of read pairs as single entities versus separately, and AU/range structure supported by mode-dependent organization. Across the independent claims, the inventive features focus on indexing-table-driven AU identification and MaxD-controlled handling of read pairs.

Across the independent claims, the inventive coverage centers on AU-level selective identification using an indexing table containing AU start and end coordinates disjointly coded from the entropy coded AUs, and on using a dataset-header threshold MaxD that specifies a maximum pairing distance for read pairs to determine whether read pairs are coded together as a single entity or separately. The decoding claim mirrors the coding claim by parsing the same AU coordinate values and MaxD from the genomic dataset header and disjoint indexing table.

Stated Advantages

Documented Applications