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Elsevier, Biophysical Journal, 10(102), p. L37-L39, 2012

DOI: 10.1016/j.bpj.2012.04.009

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DNA Base-Calling from a Nanopore Using a Viterbi Algorithm

Journal article published in 2012 by Winston Timp, Jeffrey Comer, Aleksei Aksimentiev ORCID
This paper is available in a repository.
This paper is available in a repository.

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Abstract

Nanopore-based DNA sequencing is the most promising third-generation sequencing method. It has superior read length, speed, and sample requirements compared with state-of-the-art second-generation methods. However, base-calling still presents substantial difficulty because the resolution of the technique is limited compared with the measured signal/noise ratio. Here we demonstrate a method to decode 3-bp-resolution nanopore electrical measurements into a DNA sequence using a Hidden Markov model. This method shows tremendous potential for accuracy (∼98%), even with a poor signal/noise ratio.