Nanopore basecalling from a perspective of instance segmentation.

ABSTRACT:

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

SUBMITTER: Zhang YZ 

PROVIDER: S-EPMC7178565 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature