R&D: Synchronization and Asymmetric Error Correction for Nanopore Sequencing

IEEE Xplore has published, in 2021 IEEE International Conference on Consumer Electronics-Taiwan (ICCE-TW) proceedings, an article written by Ryosuke Nakata, and Haruhiko Kaneko, School of Computing, Tokyo Institute of Technology Meguro-ku, Tokyo.

Abstract: “Nanopore sequencing is prone to synchronization and asymmetric substitution errors. Error correction coding suitable for correcting these errors is required to improve the reliability of DNA storage. This paper defines a channel model which can express both synchronization and asymmetric errors. We also show an concatenated coding using outer LDPC code and inner marker, and present a decoding algorithm based on a belief propagation on factor graph. Numerical results show that, for evaluated channel parameters, the error rate is minimized when the marker interval is 5 and the oversampling factor is 10.“