ORCOM

ORCOM compresses FASTQ sequencing reads by exploiting overlaps using a minimizer-based, disk-backed approach to reduce storage requirements for high-coverage genomic datasets.

Key Features:

• High Compression Efficiency: Achieves 0.317 bits per base, compressing a 134.0 Gbp human genome at ~45-fold coverage into 5.31 GB of storage.
• Handling Redundancy in Overlapping Reads: Captures redundancy between overlapping reads using a disk-based approach, addressing memory constraints encountered by many FASTQ compressors.
• Minimizers-Based Approach: Uses minimizers to identify representative patterns within DNA sequences and enhance compression of overlapping regions.
• Disk-Based Solution: Utilizes disk storage rather than relying solely on main memory to handle large, high-coverage sequencing datasets.
• Parallelization Capability: Algorithm design supports easy parallelization for multi-core and distributed computing environments.

Scientific Applications:

• Large-Scale Genomic Data Storage: Reduces storage and transfer requirements for high-coverage sequencing projects, exemplified by a 134.0 Gbp human genome at 45× coverage.
• Downstream Genomic Analyses: Enables efficient data management for workflows such as genome assembly, variant calling, and comparative genomics.

Methodology:

Applies minimizers to identify and compress overlapping regions within sequencing reads, employs a disk-based redundancy-capture scheme, and supports parallelized execution.