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

TL;DR

This paper develops efficient reconstruction codes for sequences affected by one deletion and one substitution, reducing redundancy for small numbers of noisy reads compared to existing methods.

Contribution

It introduces new reconstruction codes with minimized redundancy for small fixed numbers of noisy reads, improving upon previous bounds especially for N=5, 9, 11, and 14.

Findings

Redundancy for N=5 is reduced to 3 log n + 4 bits.

Redundancy for N=9 is improved to 2 log n + 12 log log n + O(1).

Redundancy for N=14 is achieved at log n + 3 bits.

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 $1\le N<N'$, an $(n, N; \mathcal{B})$-reconstruction code is also an $(n, N'; \mathcal{B})$-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.