cuteSV-OL: a real-time structural variation detection framework for nanopore sequencing devices

TL;DR

cuteSV-OL is a real-time framework for detecting structural variations in nanopore sequencing data, improving speed and efficiency for clinical use.

Contribution

cuteSV-OL integrates real-time SV detection directly into sequencing devices, enabling faster analysis and early termination of sequencing.

Findings

cuteSV-OL performs real-time SV calling during sequencing on a standard desktop computer.

It achieves performance comparable to offline methods while reducing time and cost.

The framework includes a module to evaluate SV detection rates and decide when to stop sequencing.

Abstract

Nanopore sequencing technology enables real-time sequencing and is widely used in rapid detection applications. However, in clinical scenarios, existing structural variant (SV) detection tools typically separate sequencing from computation, limiting their timeliness for clinical applications. To address this, we introduce cuteSV-OL, a novel framework designed for real-time SV discovery, which can be embedded within nanopore sequencing instruments to analyze data concurrently with its generation. Additionally, cuteSV-OL features a real-time SV detection rate evaluation module, allowing users to terminate sequencing early when appropriate, thereby reducing time and cost. Experimental results show that on a standard desktop computer, cuteSV-OL can perform real-time analysis during sequencing and complete SV calling within min after sequencing ends, achieving performance comparable to offline methods. This approach has the potential to enhance rapid clinical diagnostics.

cuteSV-OL is released under the MIT license and is available at https://github.com/gwmHIT/cuteSV-OL. It can also be installed via Bioconda or accessed through https://doi.org/10.5281/zenodo.17777436.

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