ReviewiMeta2023
Strategies and tools in illumina and nanopore-integrated metagenomic analysis of microbiome data.
Review in iMeta, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- Characterizing the epidemiology ofEmerging microbes & infections · 2025Article
- MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.Nucleic acids research · 2025Article
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- Towards the integration of antibiotic resistance gene mobility into environmental surveillance and risk assessment.npj antimicrobials and resistance · 2025Review
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Advances in Wastewater-Based Epidemiology for Pandemic Surveillance: Methodological Frameworks and Future Perspectives.Microorganisms · 2025Review
- Nanopore Environmental Analysis.JACS Au · 2025Review
- Long-Read Sequencing Outperforms Short-Read Sequencing in Detecting Most Structural Variations.Serican journal of medicine · 2025Article
- AI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery.Frontiers in microbiology · 2025Review
- Three-year nationwide survey of microbiology laboratory equipment conditions in China's CDC: setting new benchmarks.Frontiers in public health · 2025Article
- Nanopore targeted sequencing in lower respiratory infections: a retrospective study on diagnostic applications, clinical characterization, and antimicrobial guidance.Frontiers in cellular and infection microbiology · 2025Article
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.ACS synthetic biology · 2024Article
- Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.Microorganisms · 2024Review
- MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.Briefings in bioinformatics · 2024Article
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.bioRxiv : the preprint server for biology · 2024Article
- Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation.Environmental microbiome · 2024Article
- PlasCAT: Plasmid Cloud Assembly Tool.Bioinformatics (Oxford, England) · 2024Article
- Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence.Neural regeneration research · 2024Review
- Advances in multi-omics integrated analysis methods based on the gut microbiome and their applications.Frontiers in microbiology · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomic strategy serves as the foundation for the ecological exploration of novel bioresources (e.g., industrial enzymes and bioactive molecules) and biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. Recent advancements in sequencing technology have fostered rapid development in the field of microbiome research where an increasing number of studies have applied both illumina short reads (SRs) and nanopore long reads (LRs) sequencing in their metagenomic workflow. However, given the high complexity of an environmental microbiome data set and the bioinformatic challenges caused by the unique features of these sequencing technologies, integrating SRs and LRs is not as straightforward as one might assume. The fast renewal of existing tools and growing diversity of new algorithms make access to this field even more difficult. Therefore, here we systematically summarized the complete workflow from DNA extraction to data processing strategies for applying illumina and nanopore-integrated metagenomics in the investigation in environmental microbiomes. Overall, this review aims to provide a timely knowledge framework for researchers that are interested in or are struggling with the SRs and LRs integration in their metagenomic analysis. The discussions presented will facilitate improved ecological understanding of community functionalities and assembly of natural, engineered, and human microbiomes, benefiting researchers from multiple disciplines.
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Registered trials
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.