Hidden Markov model-based DNA code design for nanopore sequencers

Nanopore sequencers are devices that can read DNA molecules by interpreting a characteristic electrical signal they generate as they pass through very small openings called nanopores. In this dissertation, we consider the design of DNA codes for nanopore sequencers for their potential use as a reading device in DNA-based data storage systems. We study error performance guarantees using the nanopore signature of DNA sequences and demonstrate that we can construct long DNA codes that robust against noise and irregularly timed signal transitions. We also propose algorithms to estimate these signatures to future-proof our code design for nanopore sequencers.