G-SQZ

G-SQZ compresses high-throughput sequencing reads using a Huffman coding-based representation to reduce storage size while preserving read order and enabling selective access.

Key Features:

• Huffman coding-based representation: Implements a Huffman coding-based representation scheme for sequencing reads.
• Compression ratios: Achieves 65%–81% reduction in data size on benchmark datasets.
• Order preservation: Maintains the relative order of sequencing reads during compression.
• Selective access: Supports selective access to compressed data without scanning or decoding from the start.
• Encoding integrity: Uses an encoding scheme that preserves sequencing read integrity while delivering substantial compression.

Scientific Applications:

• High-throughput sequencing data storage: Reduces storage requirements for data generated by high-throughput sequencing instruments.
• Large-scale sequencing projects: Enables efficient retrieval and selective access in large-scale sequencing projects.
• Genomic research and bioinformatics: Facilitates downstream genomic research and bioinformatics analyses that rely on preserved read order.

Methodology:

Uses a Huffman coding-based representation and an order-preserving encoding that supports selective access without scanning or decoding from the start; benchmarks report 65%–81% compression on tested datasets.