DNA base-calling from a nanopore using a Viterbi algorithm.
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.
Winston
W
Timp
Jeffrey
J
Comer
Aleksei
A
Aksimentiev
D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D004560:Electricity; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D008390:Markov Chains; D058608:Nanopores; D017422:Sequence Analysis, DNA / Q000379:methods*; D059629:Signal-To-Noise Ratio
D004247:DNA