DNA base-calling from a nanopore using a viterbi algorithm

Winston Timp, Jeffrey Comer, Aleksei Aksimentiev

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)L37-L39
JournalBiophysical journal
Issue number10
StatePublished - May 16 2012

ASJC Scopus subject areas

  • Biophysics


Dive into the research topics of 'DNA base-calling from a nanopore using a viterbi algorithm'. Together they form a unique fingerprint.

Cite this