Pantheon-DNA: Versatile encoding-decoding system with integrated adaptive NGS preprocessing algorithms for DNA data...

Area of Science:

• Biotechnology
• Bioinformatics
• Data Storage

Background:

• DNA data storage offers high density but faces scalability and error challenges.
• Repetitive DNA sequences can cause molecular-level errors and complicate data processing.
• Efficiently managing and retrieving large datasets from DNA is crucial for practical applications.

Purpose of the Study:

• To introduce Pantheon-DNA, an end-to-end processing pipeline for DNA data storage.
• To address scalability and efficiency challenges in DNA data storage systems.
• To improve data retrievability and reliability in DNA-based storage.

Main Methods:

• Developed a data arrangement scheme and randomization procedure to prevent problematic DNA sequence patterns.
• Implemented a block data architecture for enhanced parallel processing and retrieval.
• Utilized prior knowledge of encoded data structure to simplify preprocessing and reduce computational complexity.

Main Results:

• Achieved ≥99.996% data retrievability at 10× coverage under both Low Error Rate (LER) and High Error Rate (HER) conditions.
• Successfully encoded and decoded 1.59 MB of data containing multiple files in a synthesis and sequencing experiment.
• Demonstrated reduced computational complexity and simplified clustering routines through the preprocessing pipeline.

Conclusions:

• Pantheon-DNA effectively addresses scalability and efficiency in DNA data storage.
• The proposed methods enhance data reliability and retrievability, validated by experimental results.
• Future work will focus on improving error correction, especially for indel recovery, and optimizing preprocessing.