Salami Slicing Trellis for Synchronization Errors in DNA Coding

Abstract

On top of substitution errors, DNA storage channels suffer from both insertions and deletions at the same time. It is therefore important to develop error-correcting codes with efficient encoders and decoders that can combat all three types of noise. This paper introduces the salami-slicing trellis, a decision-feedback trellis that computes bitwise posterior probabilities along each strand and is coupled with polar codes across strands. The decoder alternates between advancing the trellises by one position and polar-decoding the resulting cross-strand slice, feeding the decoded bits back to the trellises for the next position. Simulations suggest that the resulting coding scheme approaches the conjectured capacity of the substitution-insertion-deletion channel.