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

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. Enrich...

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Autores principales: Martin, Samuel, Heavens, Darren, Lan, Yuxuan, Horsfield, Samuel, Clark, Matthew D., Leggett, Richard M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8785595/
https://www.ncbi.nlm.nih.gov/pubmed/35067223
http://dx.doi.org/10.1186/s13059-021-02582-x
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author Martin, Samuel
Heavens, Darren
Lan, Yuxuan
Horsfield, Samuel
Clark, Matthew D.
Leggett, Richard M.
author_facet Martin, Samuel
Heavens, Darren
Lan, Yuxuan
Horsfield, Samuel
Clark, Matthew D.
Leggett, Richard M.
author_sort Martin, Samuel
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02582-x.
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spelling pubmed-87855952022-01-24 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. Genome Biol Method 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02582-x. BioMed Central 2022-01-24 /pmc/articles/PMC8785595/ /pubmed/35067223 http://dx.doi.org/10.1186/s13059-021-02582-x Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://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.
spellingShingle Method
Martin, Samuel
Heavens, Darren
Lan, Yuxuan
Horsfield, Samuel
Clark, Matthew D.
Leggett, Richard M.
Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
title Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
title_full Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
title_fullStr Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
title_full_unstemmed Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
title_short Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
title_sort nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8785595/
https://www.ncbi.nlm.nih.gov/pubmed/35067223
http://dx.doi.org/10.1186/s13059-021-02582-x
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