SimReadUntil for benchmarking selective sequencing algorithms on ONT devices
Open access
Date
2024-05Type
- Journal Article
ETH Bibliography
yes
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Abstract
MOTIVATION: The Oxford Nanopore Technologies (ONT) ReadUntil API enables selective sequencing, which aims to selectively favor interesting over uninteresting reads, e.g. to deplete or enrich certain genomic regions. The performance gain depends on the selective sequencing decision-making algorithm (SSDA) which decides whether to reject a read, stop receiving a read, or wait for more data. Since real runs are time-consuming and costly, simulating the ONT sequencer with support for the ReadUntil API is highly beneficial for comparing and optimizing new SSDAs. Existing software like MinKNOW and UNCALLED only return raw signal data, are memory-intensive, require huge and often unavailable multi-fast5 files (≥100GB) and are not clearly documented. RESULTS: We present the ONT device simulator SimReadUntil that takes a set of full reads as input, distributes them to channels and plays them back in real time including mux scans, channel gaps and blockages, and allows to reject reads as well as stop receiving data from them. Our modified ReadUntil API provides the basecalled reads rather than the raw signal, reducing computational load and focusing on the SSDA rather than on basecalling. Tuning the parameters of tools like ReadFish and ReadBouncer becomes easier because a GPU for basecalling is no longer required. We offer various methods to extract simulation parameters from a sequencing summary file and adapt ReadFish to replicate one of their enrichment experiments. SimReadUntil's gRPC interface allows standardized interaction with a wide range of programming languages. AVAILABILITY AND IMPLEMENTATION: Code and fully worked examples are available on GitHub (https://github.com/ratschlab/sim_read_until). Show more
Permanent link
https://doi.org/10.3929/ethz-b-000672216Publication status
publishedExternal links
Journal / series
BioinformaticsVolume
Pages / Article No.
Publisher
American Physical SocietyFunding
200550 - Dynamic reference indexes for selective sequencing with application to diagnostics (SNF)
Related publications and datasets
Is new version of: http://hdl.handle.net/20.500.11850/653797
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ETH Bibliography
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