ArticleScientific reports2020
Assembly methods for nanopore-based metagenomic sequencing: a comparative study.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 116 citations in OpenAlex.
- HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.Nucleic acids research · 2026Article
- Benchmarking genome assemblers for four bacterial models based on contiguity, correctness, and completeness.Scientific reports · 2025Article
- How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.Applied and environmental microbiology · 2025Article
- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- Comparative Meta-Analysis of Long-Read and Short-Read Sequencing for Metagenomic Profiling of the Lower Respiratory Tract Infections.Microorganisms · 2025Review
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- Can Metagenomic Analyses Be Used Effectively in Safe Food Production?Food science & nutrition · 2025Review
- Ultra pure high molecular weight DNA from soil for Nanopore shotgun metagenomics and metabarcoding sequencing.MethodsX · 2025Article
- Comparison of nanopore with illumina whole genome assemblies of the Epstein-Barr virus in Burkitt lymphoma.Scientific reports · 2025Article
- Bioinformatic strategies in metagenomics of chronic prostatitis.World journal of urology · 2025Article
- Comparison of Nanopore with Illumina Whole Genome Assemblies of the Epstein-Barr Virus in Burkitt Lymphoma.medRxiv : the preprint server for health sciences · 2025Article
- Environmental community transcriptomics: strategies and struggles.Briefings in functional genomics · 2025Review
- Article
- Impact of sample multiplexing on detection of bacteria and antimicrobial resistance genes in pig microbiomes using long-read sequencing.Frontiers in microbiology · 2025Article
- Metagenomic assemblies tend to break around antibiotic resistance genes.BMC genomics · 2024Article
- HyLight: Strain aware assembly of low coverage metagenomes.Nature communications · 2024Article
- Nanopore R10.4 metagenomic detection of blaNature communications · 2024Article
- Establishing African genomics and bioinformatics programs through annual regional workshops.Nature genetics · 2024Review
- Article
- Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates.BMC genomics · 2024Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.