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Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

dc.contributor.authorMartin, Samuel
dc.contributor.authorHeavens, Darren
dc.contributor.authorLan, Yuxuan
dc.contributor.authorHorsfield, Samuel
dc.contributor.authorClark, Matthew D
dc.contributor.authorLeggett, Richard M
dc.date.accessioned2025-04-23T09:30:17Z
dc.date.available2025-04-23T09:30:17Z
dc.date.issued2022-01-24
dc.date.submitted2021-05-08
dc.identifier.citationMartin, S., Heavens, D., Lan, Y. et al. Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples. Genome Biol 23, 11 (2022). https://doi.org/10.1186/s13059-021-02582-xen_US
dc.identifier.issn1474-760X
dc.identifier.doi10.1186/s13059-021-02582-x
dc.identifier.urihttp://hdl.handle.net/10141/623287
dc.description.abstractAdaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms. To test its potential for enrichment of rarer species within metagenomic samples, we create a synthetic mock community and construct sequencing libraries with a range of mean read lengths. Enrichment is up to 13.87-fold for the least abundant species in the longest read length library; factoring in reduced yields from rejecting molecules the calculated efficiency raises this to 4.93-fold. Finally, we introduce a mathematical model of enrichment based on molecule length and relative abundance, whose predictions correlate strongly with mock and complex real-world microbial communities.en_US
dc.language.isoenen_US
dc.publisherSpringer Science and Business Media LLCen_US
dc.rightsopenAccessen_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/deed.en
dc.titleNanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samplesen_US
dc.typeJournal Articleen_US
dc.identifier.eissn1474-760X
dc.identifier.journalGenome Biologyen_US
dc.date.updated2025-04-07T15:20:55Z
dc.identifier.volume23en_US
dc.identifier.issue1en_US
dc.identifier.startpage11-en_US
elements.import.authorMartin, Samuel
elements.import.authorHeavens, Darren
elements.import.authorLan, Yuxuan
elements.import.authorHorsfield, Samuel
elements.import.authorClark, Matthew D
elements.import.authorLeggett, Richard M
dc.description.nhmCopyright © The Author(s). 2022 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. The attached file is the published version of the article.en_US
dc.description.nhmNHM Repository
dc.subject.nhmnanoporeen_US
dc.subject.nhmadaptive samplingen_US
dc.subject.nhmReadUntilen_US
dc.subject.nhmmetagenomicsen_US
dc.subject.nhmsequencingen_US
dc.subject.nhmenrichmenten_US
refterms.dateFOA2025-04-23T09:30:19Z


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