SimReadUntil for benchmarking selective sequencing algorithms on ONT devices

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• Oxford Nanopore Technologies (ONT) ReadUntil API facilitates selective sequencing for genomic enrichment or depletion.
• Optimizing selective sequencing decision-making algorithms (SSDAs) is crucial for performance but hindered by costly and time-consuming real sequencing runs.
• Existing simulation tools are memory-intensive, require large data files, and focus on raw signal data, complicating SSDA development.

Purpose of the Study:

• To develop a novel ONT device simulator, SimReadUntil, supporting the ReadUntil API for efficient SSDA evaluation.
• To provide a simulation environment that reduces computational load by using basecalled reads instead of raw signals.
• To facilitate easier parameter tuning for SSDA tools like ReadFish and ReadBouncer without requiring GPU-accelerated basecalling.

Main Methods:

• SimReadUntil simulates ONT sequencing by playing back full reads in real-time, including channel noise and blockages.
• The simulator allows for read rejection and termination of data reception, mimicking the ReadUntil API functionality.
• A gRPC interface enables standardized interaction across various programming languages, and methods are provided to extract simulation parameters from sequencing summary files.

Main Results:

• SimReadUntil successfully simulates ONT selective sequencing, providing basecalled reads for direct SSDA evaluation.
• The simulator reduces computational requirements, making SSDA development more accessible by removing the need for GPUs.
• The tool was adapted to replicate an enrichment experiment using ReadFish, demonstrating its practical application.

Conclusions:

• SimReadUntil offers a valuable, efficient, and accessible platform for developing and optimizing selective sequencing strategies on ONT devices.
• The simulator streamlines the workflow for researchers, accelerating the advancement of bioinformatics tools for targeted sequencing applications.
• Open-source availability on GitHub promotes collaborative development and wider adoption within the scientific community.