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Accuracy and Completeness of Long Read Metagenomic Assemblies

Microbes influence the surrounding environment and contribute to human health. Metagenomics can be used as a tool to explore the interactions between microbes. Metagenomic assemblies built using long read nanopore data depend on the read level accuracy. The read level accuracy of nanopore sequencing...

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Autores principales: Buttler, Jeremy, Drown, Devin M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9861289/
https://www.ncbi.nlm.nih.gov/pubmed/36677391
http://dx.doi.org/10.3390/microorganisms11010096
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author Buttler, Jeremy
Drown, Devin M.
author_facet Buttler, Jeremy
Drown, Devin M.
author_sort Buttler, Jeremy
collection PubMed
description Microbes influence the surrounding environment and contribute to human health. Metagenomics can be used as a tool to explore the interactions between microbes. Metagenomic assemblies built using long read nanopore data depend on the read level accuracy. The read level accuracy of nanopore sequencing has made dramatic improvements over the past several years. However, we do not know if the increased read level accuracy allows for faster assemblers to make as accurate metagenomic assemblies as slower assemblers. Here, we present the results of a benchmarking study comparing three commonly used long read assemblers, Flye, Raven, and Redbean. We used a prepared DNA standard of seven bacteria as our input community. We prepared a sequencing library using a VolTRAX V2 and sequenced using a MinION mk1b. We basecalled with Guppy v5.0.7 using the super-accuracy model. We found that increasing read depth benefited each of the assemblers, and nearly complete community member chromosomes were assembled with as little as 10× read depth. Polishing assemblies using Medaka had a predictable improvement in quality. We found Flye to be the most robust across taxa and was the most effective assembler for recovering plasmids. Based on Flye’s consistency for chromosomes and increased effectiveness at assembling plasmids, we would recommend using Flye in future metagenomic studies.
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spelling pubmed-98612892023-01-22 Accuracy and Completeness of Long Read Metagenomic Assemblies Buttler, Jeremy Drown, Devin M. Microorganisms Article Microbes influence the surrounding environment and contribute to human health. Metagenomics can be used as a tool to explore the interactions between microbes. Metagenomic assemblies built using long read nanopore data depend on the read level accuracy. The read level accuracy of nanopore sequencing has made dramatic improvements over the past several years. However, we do not know if the increased read level accuracy allows for faster assemblers to make as accurate metagenomic assemblies as slower assemblers. Here, we present the results of a benchmarking study comparing three commonly used long read assemblers, Flye, Raven, and Redbean. We used a prepared DNA standard of seven bacteria as our input community. We prepared a sequencing library using a VolTRAX V2 and sequenced using a MinION mk1b. We basecalled with Guppy v5.0.7 using the super-accuracy model. We found that increasing read depth benefited each of the assemblers, and nearly complete community member chromosomes were assembled with as little as 10× read depth. Polishing assemblies using Medaka had a predictable improvement in quality. We found Flye to be the most robust across taxa and was the most effective assembler for recovering plasmids. Based on Flye’s consistency for chromosomes and increased effectiveness at assembling plasmids, we would recommend using Flye in future metagenomic studies. MDPI 2022-12-30 /pmc/articles/PMC9861289/ /pubmed/36677391 http://dx.doi.org/10.3390/microorganisms11010096 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Buttler, Jeremy
Drown, Devin M.
Accuracy and Completeness of Long Read Metagenomic Assemblies
title Accuracy and Completeness of Long Read Metagenomic Assemblies
title_full Accuracy and Completeness of Long Read Metagenomic Assemblies
title_fullStr Accuracy and Completeness of Long Read Metagenomic Assemblies
title_full_unstemmed Accuracy and Completeness of Long Read Metagenomic Assemblies
title_short Accuracy and Completeness of Long Read Metagenomic Assemblies
title_sort accuracy and completeness of long read metagenomic assemblies
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9861289/
https://www.ncbi.nlm.nih.gov/pubmed/36677391
http://dx.doi.org/10.3390/microorganisms11010096
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