Journal Article

Nanopore basecalling from a perspective of instance segmentation

Miyano, Satoru, Shibuya, Tetsuo, Imoto, Seiya, Tremmel, Georg, Yamaguchi, Rui, Akdemir, Arda, Zhang, Yao-zhong

2020

Overview

Background Nanopore sequencing is a rapidly developing third-generation sequencing technology, which can generate long nucleotide reads of molecules within a portable device in real-time. Through detecting the change of ion currency signals during a DNA/RNA fragment’s pass through a nanopore, genotypes are determined. Currently, the accuracy of nanopore basecalling has a higher error rate than the basecalling of short-read sequencing. Through utilizing deep neural networks, the-state-of-the art nanopore basecallers achieve basecalling accuracy in a range from 85% to 95%. Result In this work, we proposed a novel basecalling approach from a perspective of instance segmentation. Different from previous approaches of doing typical sequence labeling, we formulated the basecalling problem as a multi-label segmentation task. Meanwhile, we proposed a refined U-net model which we call UR-net that can model sequential dependencies for a one-dimensional segmentation task. The experiment results show that the proposed basecaller URnano achieves competitive results on the in-species data, compared to the recently proposed CTC-featured basecallers. Conclusion Our results show that formulating the basecalling problem as a one-dimensional segmentation task is a promising approach, which does basecalling and segmentation jointly.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Accuracy / Algorithms / Artificial neural networks / Bioinformatics / Biomedical and Life Sciences / Cable television broadcasting industry / Change detection / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Deep learning / Deoxyribonucleic acid / DNA / DNA - genetics / Genomes / Genotypes / Instance segmentation / Life Sciences / Methodology / Microarrays / Nanopore basecalling / Nanopore Sequencing - methods / Neural networks / Neural Networks, Computer / Nucleotides / Porosity / Portable equipment / Ribonucleic acid / RNA / RNA - genetics / Segmentation / UR-net