nanopore sequencing
The noisy nanopore channel is introduced as a model of the nanopore sequencer in DNA storage that includes inter-symbol interference, sample duplications, and measurement noise. Information rates of the noisy nanopore channel with Markov sources are computed numerically based on a Monte Carlo technique that builds upon existing techniques for finite-state channels. However, the analogous technique for channels with duplications poses a challenging problem from an algorithmic perspective.
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In an infectious disease outbreak the identification of pathogen genome sequence variants provides epidemiologists with high-resolution transmission diagnostics that can help cluster patients; identify cohorts of individuals who need testing; and identify new variants that may compromise existing vaccines, therapeutics, and low-resolution detection diagnostics. The Oxford Nanopore MinION™ is a uniquely portable nucleic acid sequencing device that has been used in limited-resource settings for this purpose, e.g., during the 2014-2016 outbreak of Ebolavirus (EBOV) disease in Africa. We desc
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