DNA base-calling from a nanopore using a Viterbi algorithm

Winston Timp, Jeffrey Comer, and Aleksei Aksimentiev
Biophys J 102(10) L37-9 (2012)
DOI:10.1016/j.bpj.2012.04.009  PMID:22677395  BibTex

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.