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

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Nanopore adaptive sampling a ...

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Authors

Martin, Samuel
Heavens, Darren
Lan, Yuxuan
Horsfield, Samuel
Clark, Matthew D
Leggett, Richard M

Issue date

2022-01-24

Submitted date

2021-05-08

Subject Terms

nanopore
adaptive sampling
ReadUntil
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.

Citation

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

Type

Journal Article

Item Description

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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ISSN

1474-760X

EISSN

1474-760X

Collections

Life sciences

Except where otherwise noted, this item's license is described as openAccess