Multi-strand Reconstruction from Substrings

Abstract

The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup of this problem where multiple strings are reconstructed together. Given a multiset S of strings, all their substrings of some fixed length ℓ, defined as the ℓ-profile of S, are received and the goal is to reconstruct all strings in S. A multi-strand ℓ-reconstruction code is a set of multisets such that every element S can be reconstructed from its ℓ-profile. Given the number of strings k and their length n, we first find a lower bound on the value of ℓ necessary for existence of multi-strand ℓ-reconstruction codes with non-vanishing asymptotic rate. We then present two constructions of such codes and show that their rates approach 1 for values of ℓ that asymptotically behave like the lower bound.