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 (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore sequencers can acquire long reads, the high error rates (20%-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 (non-linear) inter-symbol interference, deletions, as well as random response. These information bounds have two-fold application: (1) The decoding rate with a uniform input distribution can be used to calculate the average size of the plausible list of DNA sequences given an observed current trace. This bound can be used to benchmark existing base-calling algorithms, as well as serving a performance objective to design better nanopores. (2) When the nanopore sequencer is used as a reader in a DNA storage system, the storage capacity is quantified by our bounds

Write Channel Model for Bit-Patterned Media Recording

We propose a new write channel model for bit-patterned media recording that reflects the data dependence of write synchronization errors. It is shown that this model accommodates both substitution-like errors and insertion-deletion errors whose statistics are determined by an underlying channel state process. We study information theoretic properties of the write channel model, including the capacity, symmetric information rate, Markov-1 rate and the zero-error capacity.Comment: 11 pages, 12 figures, journa

Gaussian Belief Propagation Based Multiuser Detection

In this work, we present a novel construction for solving the linear multiuser detection problem using the Gaussian Belief Propagation algorithm. Our algorithm yields an efficient, iterative and distributed implementation of the MMSE detector. We compare our algorithm's performance to a recent result and show an improved memory consumption, reduced computation steps and a reduction in the number of sent messages. We prove that recent work by Montanari et al. is an instance of our general algorithm, providing new convergence results for both algorithms.Comment: 6 pages, 1 figures, appeared in the 2008 IEEE International Symposium on Information Theory, Toronto, July 200