From spacecraft ranging to massive DNA data storage: Composite ranging codes as indices and error correction...

Area of Science:

• Biotechnology
• Data Storage
• Bioinformatics

Background:

• DNA data storage offers a promising archival medium but faces challenges in data retrieval due to unordered strands, indexing needs, and error proneness.
• Efficiently accessing large datasets stored on DNA requires robust indexing and error correction mechanisms.

Purpose of the Study:

• To develop a novel indexing and progressive recovery framework for massive DNA data storage.
• To address the critical challenge of retrieving large-scale data from error-prone DNA strands.

Main Methods:

• Proposed an accompanying indexing and progressive recovery framework utilizing specialized long composite ranging codes (LCRCs).
• Employed short fractions of LCRCs as indices for data ranging from megabytes to petabytes.
• Developed correlation and alignment strategies for rapid and reliable data recovery, respectively.

Main Results:

• Demonstrated the framework's scalability to the petabyte level through simulations.
• Achieved low-coverage recovery using progressive error correction.
• Successfully recovered 12.87-megabyte files in approximately 20 minutes with 3.66× coverage and a ~4.9% error rate using a nanopore sequencer.

Conclusions:

• The proposed framework offers a universal and practical strategy for massive DNA data storage.
• The LCRC-based indexing and recovery system enhances data retrieval efficiency and reliability.
• This approach enables real-time, read-by-read decoding for practical DNA data archiving.