Models and information-theoretic bounds for nanopore sequencing

Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (similar to 50,000 bases) unlike most current sequencers which can only read hundreds of bases. While nanopore sequencers can acquire long reads, the high error rates (approximate to 30%) pose a technical challenge. In a nanopore sequencer, a DNA is migrated through a nanopore and current variations are measured. The DNA sequence is inferred from this observed current pattern using an algorithm called a base-caller. In this paper, we propose a mathematical model for the "channel" from the input DNA sequence to the observed current, and calculate bounds on the information extraction capacity of the nanopore sequencer. This model incorporates impairments like inter-symbol interference, deletions, as well as random response. The practical application of such information bounds is two-fold: (1) benchmarking present base-calling algorithms, and (2) offering an optimization objective for designing better nanopore sequencers.