Implementation of a nanopore DNA base-caller

The use of nanopore for the sequencing of biopolymers, such as DNA, have the potential to revolutionize the field of molecular biology. Electrophoresis is used to transport of the biopolymers through a nanopore embedded in membrane. During the translocation events, the physcochemical propreties of the biopolymers will modulate the current intensity. The characteristic changes in the electric current density should allow for the identification of biopolymer. Unfortunately, current techonlogies suffer from a high error rate.

In this project, the candidate will have to first implement a denoising pipeline base the theory of Singular Spectrum Analysis. A base caller will then have to be design in order to extract the DNA sequence from the denoised current. The candidate is expected to have a strong background in signal processing.

Supervised by Thomas Lemmin

thomas.lemmin@inf.ethz.ch

References

  • [1] Yanxiao Feng, Yuechuan Zhang, Cuifeng Ying, Deqiang Wang, Chunlei Du, Nanopore-based Fourth-generation DNA Sequencing Technology GPB