{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T16:05:33Z","timestamp":1778774733568,"version":"3.51.4"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,4,11]],"date-time":"2024-04-11T00:00:00Z","timestamp":1712793600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100022491","name":"Max Planck ETH Center for Learning Systems","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100022491","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100003351","name":"SNF","doi-asserted-by":"publisher","award":["#200550"],"award-info":[{"award-number":["#200550"]}],"id":[{"id":"10.13039\/100003351","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>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 (\u2265100GB) and are not clearly documented.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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\u2019s gRPC interface allows standardized interaction with a wide range of programming languages.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Code and fully worked examples are available on GitHub (https:\/\/github.com\/ratschlab\/sim_read_until).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae199","type":"journal-article","created":{"date-parts":[[2024,4,9]],"date-time":"2024-04-09T15:42:52Z","timestamp":1712677372000},"source":"Crossref","is-referenced-by-count":2,"title":["SimReadUntil for benchmarking selective sequencing algorithms on ONT devices"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5731-484X","authenticated-orcid":false,"given":"Maximilian","family":"Mordig","sequence":"first","affiliation":[{"name":"Biomedical Informatics Group, Department of Computer Science, ETH Zurich , Z\u00fcrich, 8092, Switzerland"},{"name":"Empirical Inference, Max Planck Institute for Intelligent Systems , T\u00fcbingen, 72076, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5486-8532","authenticated-orcid":false,"given":"Gunnar","family":"R\u00e4tsch","sequence":"additional","affiliation":[{"name":"Biomedical Informatics Group, Department of Computer Science, ETH Zurich , Z\u00fcrich, 8092, Switzerland"},{"name":"Biomedical Informatics Research, University Hospital Zurich , Z\u00fcrich, 8091, Switzerland"},{"name":"Swiss Institute of Bioinformatics , Lausanne, 1015, Switzerland"},{"name":"Department of Biology, ETH Zurich , Z\u00fcrich, 8092, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3411-0692","authenticated-orcid":false,"given":"Andr\u00e9","family":"Kahles","sequence":"additional","affiliation":[{"name":"Biomedical Informatics Group, Department of Computer Science, ETH Zurich , Z\u00fcrich, 8092, Switzerland"},{"name":"Biomedical Informatics Research, University Hospital Zurich , Z\u00fcrich, 8091, Switzerland"},{"name":"Swiss Institute of Bioinformatics , Lausanne, 1015, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,4,11]]},"reference":[{"key":"2024050222534343200_btae199-B1","doi-asserted-by":"publisher","first-page":"i297","DOI":"10.1093\/bioinformatics\/btad272","article-title":"RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes","volume":"39","author":"Firtina","year":"2023","journal-title":"Bioinformatics"},{"key":"2024050222534343200_btae199-B2","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/s41587-020-0731-9","article-title":"Targeted nanopore sequencing by real-time mapping of raw electrical signal with 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