ArticleNAR genomics and bioinformatics2025
Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.
Article in NAR genomics and bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Pathogen genome enrichment sequencing to support a city-wide Legionnaires' disease outbreak investigation.Microbial genomics · 2026Article
- Choosing Between Short-Read 16S, Full-Length ONT 16S, and Long-Read Shotgun Metagenomics for Soil Microbiome Studies: A Critical Review of the Benchmarking Evidence.Microorganisms · 2026Review
- Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.Nature microbiology · 2026Article
- Integrative Bioinformatics Approaches in Environmental Biotechnology: A Review.TheScientificWorldJournal · 2026Review
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Authors and funding
5 authors.
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Abstract
Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but struggle to assemble complicated genome regions (e.g. repeats) compared to long-read sequence assemblies. Accurate metagenome assembly is especially challenging in diverse environments, such as soil, and long-read sequencing has been shown to improve assembly. Here, we use metagenomic data with paired long-read and short-read sequences to identify specific factors that impact genome assembly and assess their relative importance in a natural soil community. Our analysis suggests that low coverage and high sequence diversity are the two main factors leading to misassemblies in short-read data, and many of these "missed" regions tend to be variable parts of the genome, such as integrated viruses or defense system islands. Taken together, our results demonstrate that short-read metagenomes can possibly underestimate the diversity of these genome regions and that long-read sequencing can complement short-read metagenomes by improving assembly contiguity and the recovery of variable regions.
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Registered trials
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