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Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
Martin, Samuel Heavens, Darren Lan, Yuxuan Horsfield, Samuel Clark, Matthew D Leggett, Richard M
Martin, Samuel
Heavens, Darren
Lan, Yuxuan
Horsfield, Samuel
Clark, Matthew D
Leggett, Richard M
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2022-01-24
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2021-05-08
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nanopore
adaptive sampling
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metagenomics
sequencing
enrichment
adaptive sampling
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metagenomics
sequencing
enrichment
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Abstract
Adaptive 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.
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Martin, 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-x
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Copyright © 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.
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1474-760X
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1474-760X
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openAccess