New LDPC coding method improves DNA storage error correction
Orthogonal SC-LDPC Codes for the IDS Channel
Information Theory
Summary
Storing data in DNA is promising but tricky because the DNA strands can get messed up by insertions, deletions, or substitutions of letters. The authors present a new way to organize and decode data across multiple DNA strands so that each strand helps fix its neighbors, improving overall accuracy. This method works especially well for short DNA strands, like those typically used in DNA data storage. The authors show their approach beats a previous coding method for these short strands.
What this means in practice
- •For dna storage engineers: Improve error correction in short DNA strand data storage by using coupled codes that synchronize decoding across strands.
- •For data transmission specialists: Use coupling strategies from this method to enhance synchronization and error correction in channels with insertions, deletions, and substitutions.
Authors
Frederik Walter, Jessica Bariffi, Antonia Wachter-Zeh
Abstract
We propose a coding scheme for the insertion, deletion and substitution (IDS) channel tailored to the short strands of DNA-based data storage. Instead of an inner synchronisation code, a spatially coupled LDPC (SC-LDPC) code is placed across the strands, with its coupling axis aligned to the position along the strands. Every decoded position thus becomes an anchor to synchronise the neighbouring strands. The decoding waves of the SC-LDPC code carry these anchors from both ends of the strands towards the middle. We bound the achievable rate from above by the information rate of a single strand and from below by that of a separated receiver. For strands of 100 nucleotides (the relevant regime for DNA-based data storage), our scheme outperforms a rate-matched concatenated construction.