GVC

GVC compresses gene sequence variations generated by high-throughput sequencing technologies while preserving random access to enable efficient storage and retrieval of genotype data.

Key Features:

• Binarization: Applies binarization to represent variation data prior to further processing.
• Joint row- and column-wise sorting: Performs joint row- and column-wise sorting of variation blocks to improve local structure for compression.
• JBIG entropy coding: Uses the image compression standard JBIG for entropy coding of the processed variation blocks.
• Random-access compression: Maintains random access to compressed variation blocks to allow retrieval of specific segments without full decompression.
• Demonstrated compression performance: Compresses 1000 Genomes Project (phase 3) genotype information from 758 GiB to 890 MiB, outperforming current state-of-the-art random-access capable methods by 21%.

Scientific Applications:

• Precision medicine: Reduces storage and enables selective retrieval of variant data used in genotype-driven clinical analyses.
• Oncology: Supports storage and access of large variant datasets relevant to cancer genomics studies.
• Food quality control: Enables compressed storage and targeted access of genetic variation data used in food quality and safety applications.
• Remote data retrieval and integration: Facilitates remote access to specific compressed genomic segments for integration with downstream applications.
• Large-scale genomic data management: Lowers storage footprint and improves manageability of population-scale genotype datasets.

Methodology:

Uses binarization, joint row- and column-wise sorting of variation blocks, and JBIG for entropy coding.