Optimization of Error Correction Schemes for DNA Synthesis and Sequencing

Despite the existence of numerous mature error correction algorithms in traditional communications, most are designed to address substitution or erasure errors in communication channels. However, due to the inherent limitations of DNA synthesis and sequencing processes, such as base insertions, deletions, substitutions, and sequence readout errors, traditional error correction algorithms from the communications field are not well-suited for DNA data storage. Optimizing these existing algorithms is essential for effective data recovery and efficient readout in DNA data storage. In this chapter, we explore strategies to optimize existing error correction algorithms for handling insertion, deletion, and substitution (IDS) errors. Additionally, enhancing the error correction capabilities of these algorithms can enable the adoption of low-cost, high-error-rate DNA synthesis technologies, ultimately reducing the cost of DNA data storage. Finally, we introduce error correction optimizations specific to DNA sequencing, where clustering and alignment techniques can further improve error correction effectiveness.