Embracing Errors is More Efficient than Avoiding Them through Constrained Coding for DNA Data Storage
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DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the number of errors, a common technique is to include constraints that avoid homopolymers (consecutive repeated nucleotides) and balance the GC content, as sequences with homopolymers and unbalanced GC contents are often associated with larger error rates. However, constrained coding comes at the cost of an increase in redundancy. An alternative (unconstrained coding) is to control the errors by randomizing the sequences, embracing errors, and paying for them with additional coding redundancy. In this paper, we determine the error regimes in which embracing errors is more efficient than constrained coding. We find that constrained coding is inefficient in most common error regimes for DNA data storage. Specifically, the error probabilities for nucleotides in homopolymers and in sequences with unbalanced GC contents must be very large for constrained coding to achieve a higher code rate than unconstrained coding.
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