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Biophys J. 2012 May 16;102(10):L37-9. doi: 10.1016/j.bpj.2012.04.009. Epub 2012 May 15.

DNA base-calling from a nanopore using a Viterbi algorithm.

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.

PMID:
22677395
PMCID:
PMC3353060
DOI:
10.1016/j.bpj.2012.04.009
[Indexed for MEDLINE]
Free PMC Article

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