# The Hybrid k-Deck Problem: Reconstructing Sequences from Short and Long Traces

## TL;DR

This paper introduces the hybrid k-deck problem, combining traditional sequence reconstruction with partial subsequences, providing bounds for the minimal k needed for accurate reconstruction, motivated by DNA sequencing applications.

## Contribution

It defines the hybrid k-deck problem, derives bounds for the minimal k in single and multiple subsequence cases, and extends classical sequence reconstruction theory.

## Key findings

- Bounds for k in single subsequence case: [log t+2, min{t+1, O(√(n(1+log t)))}]
- Extension to multiple subsequences by aggregation and applying single-trace results
- Motivated by nanopore sequencing for DNA data storage

## Abstract

We introduce a new variant of the $k$-deck problem, which in its traditional formulation asks for determining the smallest $k$ that allows one to reconstruct any binary sequence of length $n$ from the multiset of its $k$-length subsequences. In our version of the problem, termed the hybrid k-deck problem, one is given a certain number of special subsequences of the sequence of length $n - t$, $t > 0$, and the question of interest is to determine the smallest value of $k$ such that the $k$-deck, along with the subsequences, allows for reconstructing the original sequence in an error-free manner. We first consider the case that one is given a single subsequence of the sequence of length $n - t$, obtained by deleting zeros only, and seek the value of $k$ that allows for hybrid reconstruction. We prove that in this case, $k \in [\log t+2, \min\{ t+1, O(\sqrt{n \cdot (1+\log t)}) \} ]$. We then proceed to extend the single-subsequence setup to the case where one is given $M$ subsequences of length $n - t$ obtained by deleting zeroes only. In this case, we first aggregate the asymmetric traces and then invoke the single-trace results. The analysis and problem at hand are motivated by nanopore sequencing problems for DNA-based data storage.