A Converse For the Capacity of the Shotgun Sequencing Channel with Erasures

Abstract

The shotgun sequencing process involves fragmenting a long DNA sequence (input string) into numerous shorter, unordered, and overlapping segments (referred to as \emph{reads}). The reads are sequenced, and later aligned to reconstruct the original string. Viewing the sequencing process as the read-phase of a DNA storage system, the information-theoretic capacity of noise-free shotgun sequencing has been characterized in literature. Motivated by the base-wise quality scores available in practical sequencers, a recent work considered the \emph{shotgun sequencing channel with erasures}, in which the symbols in the reads are assumed to contain random erasures. Achievable rates for this channel were identified. In the present work, we obtain a converse for this channel. The arguments for the proof involve a careful analysis of a genie-aided decoder, which knows the correct locations of the reads. The converse is not tight in general. However, it meets the achievability result asymptotically in some channel parameters.