Simulating Noisy Channels in DNA Storage

Abstract

Compared to conventional storage mediums, DNA-based data storage offers benefits such as durability, high density and low energy consumption. With increased demand for DNA data storage, it has become important to quickly evaluate proposed approaches. However, experiments that involves reading and writing synthetic DNA are costly and time-consuming, thus requiring cheap and fast simulation prior to experimentation. DNA sequencing technologies such as Nanopore and Illumina have highly characteristic error profiles, and simulating them is challenging. We propose a DNA simulator for Nanopore data that improves on existing simulators by incorporating key parameters; our simulator better converges to error profiles of real data on most parameters.We show that the spatial distribution of errors within a strand is a key determinant of trace reconstruction accuracy; which is a factor that had not been considered by existing simulators.