ArticleScientific reports2021
Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Review
- Fosfomycin Resistance: An Update on the Anthropogenic Impact Through Agriculture.Pathogens (Basel, Switzerland) · 2025Review
- A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.Scientific data · 2025Article
- The surveillance of antimicrobial resistance in wastewater from a one health perspective: A global scoping and temporal review (2014-2024).One health (Amsterdam, Netherlands) · 2025Article
- Mapping the underlying drivers of resistome risk across diverse environments.Research square · 2025Article
- The food-associated resistome is shaped by processing and production environments.Nature microbiology · 2025Article
- Enhancing public health surveillance: a comparative study of platform-specific and hybrid assembly approaches in SARS-CoV-2 genome sequencing.Microbial genomics · 2025Article
- Detecting antibiotic resistance: classical, molecular, advanced bioengineering, and AI-enhanced approaches.Frontiers in microbiology · 2025Review
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- ARGContextProfiler: extracting and scoring the genomic contexts of antibiotic resistance genes using assembly graphs.Frontiers in microbiology · 2025Article
- A novel and accelerated method for integrated alignment and variant calling from short and long reads.Frontiers in bioinformatics · 2025Article
- Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes.Marine drugs · 2024Article
- MetaCompare 2.0: differential ranking of ecological and human health resistome risks.FEMS microbiology ecology · 2024Article
- Metagenomic assemblies tend to break around antibiotic resistance genes.BMC genomics · 2024Article
- HyLight: Strain aware assembly of low coverage metagenomes.Nature communications · 2024Article
- Bacterial strain sharing between humans, animals, and the environment among urban households.medRxiv : the preprint server for health sciences · 2024Article
- Capturing clinically relevantMicrobial genomics · 2024Article
- Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities.Microbiology (Reading, England) · 2024Article
- Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution.Microbiome · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the fight to limit the global spread of antibiotic resistance, the assembly of environmental metagenomes has the potential to provide rich contextual information (e.g., taxonomic hosts, carriage on mobile genetic elements) about antibiotic resistance genes (ARG) in the environment. However, computational challenges associated with assembly can impact the accuracy of downstream analyses. This work critically evaluates the impact of assembly leveraging short reads, nanopore MinION long-reads, and a combination of the two (hybrid) on ARG contextualization for ten environmental metagenomes using seven prominent assemblers (IDBA-UD, MEGAHIT, Canu, Flye, Opera-MS, metaSpades and HybridSpades). While short-read and hybrid assemblies produced similar patterns of ARG contextualization, raw or assembled long nanopore reads produced distinct patterns. Based on an in-silico spike-in experiment using real and simulated reads, we show that low to intermediate coverage species are more likely to be incorporated into chimeric contigs across all assemblers and sequencing technologies, while more abundant species produce assemblies with a greater frequency of inversions and insertion/deletions (indels). In sum, our analyses support hybrid assembly as a valuable technique for boosting the reliability and accuracy of assembly-based analyses of ARGs and neighboring genes at environmentally-relevant coverages, provided that sufficient short-read sequencing depth is achieved.
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