Icarust, a real-time simulator for Oxford Nanopore adaptive sampling.

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology and Genetics

Background:

• Oxford Nanopore Technologies (ONT) sequencers offer real-time data generation, enabling concurrent analysis during sequencing runs.
• Adaptive sampling, a feature of ONT's MinKNOW software, allows real-time decision-making on which DNA reads to sequence further.
• Developing software for adaptive sampling is resource-intensive due to consumables, sample usage, and library preparation costs.

Purpose of the Study:

• To develop a tool, Icarust, that provides more accurate approximations of nanopore sequencing runs with adaptive sampling.
• To create a realistic testing and development environment for software that utilizes the real-time capabilities of Nanopore sequencing.
• To overcome the limitations of MinKNOW's run replay functionality, which yields only partially altered sequencing outputs.

Main Methods:

• Icarust recreates essential MinKNOW endpoints required for adaptive sampling functionality.
• The tool simulates nanopore signal data for MinION or PromethION flow cell experiments from any reference genome.
• Icarust supports both R9 and R10 pore models and generates output compatible with current base-callers and analysis pipelines.

Main Results:

• Icarust enables more accurate simulation of sequencing runs compared to existing methods.
• The simulated output is compatible with downstream bioinformatics tools, facilitating software development.
• The tool provides a cost-effective and efficient environment for testing adaptive sampling software.

Conclusions:

• Icarust offers a realistic and reliable platform for developing and testing software that exploits real-time adaptive sampling in Nanopore sequencing.
• The open-source availability of Icarust (implemented in Rust with Docker support) promotes wider adoption and collaboration in the field.