Group Testing with Runlength Constraints for Topological Molecular Storage

Abstract

Motivated by applications in topological DNA-based data storage, we introduce and study a novel setting of Non-Adaptive Group Testing (NAGT) with runlength constraints on the columns of the test matrix, in the sense that any two 1's must be separated by a run of at least d 0's. We describe and analyze a probabilistic construction of a runlength-constrained scheme in the zero-error and vanishing error settings, and show that the number of tests required by this construction is optimal up to logarithmic factors in the runlength constraint d and the number of defectives k in both cases. Surprisingly, our results show that runlength-constrained NAGT is not more demanding than unconstrained NAGT when d=O(k), and that for almost all choices of d and k it is not more demanding than NAGT with a column Hamming weight constraint only. Towards obtaining runlength-constrained Quantitative NAGT (QNAGT) schemes with good parameters, we also provide lower bounds for this setting and a nearly optimal probabilistic construction of a QNAGT scheme with a column Hamming weight constraint