Correcting One Deletion and One Substitution with a Constant Number of Reads

Abstract

In this paper, we investigate the problem of designing $(n,N;\mathcal{B})$-reconstruction codes for $N\in \{14,11,9,5\}$, where $\mathcal{B}$ is the single-deletion single-substitution ball function that maps a sequence to the set of all sequences obtainable via one deletion and one substitution. Such a code is defined by the requirement that the intersection size of any two distinct single-deletion single-substitution balls is strictly less than the given number of noisy reads $N$. Note that for any $1\le N<N^{\prime }$, an $(n,N;\mathcal{B})$-reconstruction code is also an $(n,N^{\prime };\mathcal{B})$-reconstruction code. It follows that the problem of designing $(n,N;\mathcal{B})$-reconstruction codes with less redundancy becomes more challenging as $N$ decreases, particularly because the problem for $N=1$ already reduces to the coding problem of single-deletion and single-substitution correcting codes. To the best of our knowledge, most existing results focus on the case where $N$ is a linear function of $n$, while only a limited number consider constant $N$. When $N=1$, the best known $(n,1;\mathcal{B})$-reconstruction codes (single-deletion and single-substitution correcting codes) require $(4+o(1))\log n$ redundant bits. In this work, we show that this redundancy can be reduced to $3\log n+4$ when $N=5$. As $N$ increases further to $9$ and $11$, the redundancy can be improved to $2\log n+12\log \log n+O(1)$ and $\log n+12\log \log n+O(1)$, respectively. Finally, for $N=14$, we provide a reconstruction code with $\log n+3$ bits of redundancy, which is only two bits more than the best known $(n,18;\mathcal{B})$-reconstruction codes.