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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-12-01
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| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/11/1/96 |
| _version_ | 1827623121034674176 |
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| author | Jeremy Buttler Devin M. Drown |
| author_facet | Jeremy Buttler Devin M. Drown |
| author_sort | Jeremy Buttler |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T11:38:56Z |
| format | Article |
| id | doaj.art-2420eaa1b2764ceb9fa5da518189733e |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T11:38:56Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-2420eaa1b2764ceb9fa5da518189733e2023-11-30T23:36:21ZengMDPI AGMicroorganisms2076-26072022-12-011119610.3390/microorganisms11010096Accuracy and Completeness of Long Read Metagenomic AssembliesJeremy Buttler0Devin M. Drown1Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775, USADepartment of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775, USAMicrobes 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.https://www.mdpi.com/2076-2607/11/1/96nanopore sequencingbenchmarkingmicrobial communitieslong read assemblers |
| spellingShingle | Jeremy Buttler Devin M. Drown Accuracy and Completeness of Long Read Metagenomic Assemblies Microorganisms nanopore sequencing benchmarking microbial communities long read assemblers |
| 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 | nanopore sequencing benchmarking microbial communities long read assemblers |
| url | https://www.mdpi.com/2076-2607/11/1/96 |
| work_keys_str_mv | AT jeremybuttler accuracyandcompletenessoflongreadmetagenomicassemblies AT devinmdrown accuracyandcompletenessoflongreadmetagenomicassemblies |