Assembly methods for nanopore-based metagenomic sequencing: a comparative study

Abstract Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due to their potential to generate long r...

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Autores principales:	Adriel Latorre-Pérez, Pascual Villalba-Bermell, Javier Pascual, Cristina Vilanova
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ed3be38cf7654157b93e181259da1bfc
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spelling	oai:doaj.org-article:ed3be38cf7654157b93e181259da1bfc2021-12-02T18:50:57ZAssembly methods for nanopore-based metagenomic sequencing: a comparative study10.1038/s41598-020-70491-32045-2322https://doaj.org/article/ed3be38cf7654157b93e181259da1bfc2020-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-70491-3https://doaj.org/toc/2045-2322Abstract Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due to their potential to generate long reads. Nevertheless, there is a lack of updated and systematic studies evaluating the performance of different assembly tools on nanopore data. In this study, we have benchmarked the ability of different assemblers to reconstruct two different commercially-available mock communities that have been sequenced using Oxford Nanopore Technologies platforms. Among the tested tools, only metaFlye, Raven, and Canu performed well in all the datasets. These tools retrieved highly contiguous genomes (or even complete genomes) directly from the metagenomic data. Despite the intrinsic high error of nanopore sequencing, final assemblies reached high accuracy (~ 99.5 to 99.8% of consensus accuracy). Polishing strategies demonstrated to be necessary for reducing the number of indels, and this had an impact on the prediction of biosynthetic gene clusters. Correction with high quality short reads did not always result in higher quality draft assemblies. Overall, nanopore metagenomic sequencing data-adapted to MinION’s current output-proved sufficient for assembling and characterizing low-complexity microbial communities.Adriel Latorre-PérezPascual Villalba-BermellJavier PascualCristina VilanovaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-14 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Adriel Latorre-Pérez Pascual Villalba-Bermell Javier Pascual Cristina Vilanova Assembly methods for nanopore-based metagenomic sequencing: a comparative study
description	Abstract Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due to their potential to generate long reads. Nevertheless, there is a lack of updated and systematic studies evaluating the performance of different assembly tools on nanopore data. In this study, we have benchmarked the ability of different assemblers to reconstruct two different commercially-available mock communities that have been sequenced using Oxford Nanopore Technologies platforms. Among the tested tools, only metaFlye, Raven, and Canu performed well in all the datasets. These tools retrieved highly contiguous genomes (or even complete genomes) directly from the metagenomic data. Despite the intrinsic high error of nanopore sequencing, final assemblies reached high accuracy (~ 99.5 to 99.8% of consensus accuracy). Polishing strategies demonstrated to be necessary for reducing the number of indels, and this had an impact on the prediction of biosynthetic gene clusters. Correction with high quality short reads did not always result in higher quality draft assemblies. Overall, nanopore metagenomic sequencing data-adapted to MinION’s current output-proved sufficient for assembling and characterizing low-complexity microbial communities.
format	article
author	Adriel Latorre-Pérez Pascual Villalba-Bermell Javier Pascual Cristina Vilanova
author_facet	Adriel Latorre-Pérez Pascual Villalba-Bermell Javier Pascual Cristina Vilanova
author_sort	Adriel Latorre-Pérez
title	Assembly methods for nanopore-based metagenomic sequencing: a comparative study
title_short	Assembly methods for nanopore-based metagenomic sequencing: a comparative study
title_full	Assembly methods for nanopore-based metagenomic sequencing: a comparative study
title_fullStr	Assembly methods for nanopore-based metagenomic sequencing: a comparative study
title_full_unstemmed	Assembly methods for nanopore-based metagenomic sequencing: a comparative study
title_sort	assembly methods for nanopore-based metagenomic sequencing: a comparative study
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/ed3be38cf7654157b93e181259da1bfc
work_keys_str_mv	AT adriellatorreperez assemblymethodsfornanoporebasedmetagenomicsequencingacomparativestudy AT pascualvillalbabermell assemblymethodsfornanoporebasedmetagenomicsequencingacomparativestudy AT javierpascual assemblymethodsfornanoporebasedmetagenomicsequencingacomparativestudy AT cristinavilanova assemblymethodsfornanoporebasedmetagenomicsequencingacomparativestudy
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Assembly methods for nanopore-based metagenomic sequencing: a comparative study

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