Unique Reconstruction of Coded Sequences from Multiset Substring Spectra

The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded string reconstruction from multiset substring spectra, where the strings are restricted to lie in some codebook. In particular, we consider binary codebooks that allow for unique string reconstruction and propose a new method, termed repeat replacement, to create the codebook. Our contributions include algorithmic solutions for repeat replacement and constructive redundancy bounds for the underlying coding schemes. The study is motivated by applications in DNA-based data storage systems that use high throughput readout sequencers.