ReviewBriefings in bioinformatics2021
Genome-resolved metagenomics using environmental and clinical samples.
Review in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- Insights into antibiotic resistomes from gut meta-genome-assembled genomes of the free-range chickens.Veterinary and animal science · 2026Article
- Antimicrobial resistomes in plastisphere-associated microbes over aged low-density polyethylene microplastics in the Haora River of Tripura, India.Water environment research : a research publication of the Water Environment Federation · 2026Article
- Exploring microbial ecology in public swimming pools: a metagenomic investigation of community structure and environmental correlates.BMC microbiology · 2026Article
- Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials.Scientific reports · 2026Article
- Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.Interdisciplinary sciences, computational life sciences · 2026Article
- Holistic genome assembly and analysis of theIMA fungus · 2026Article
- Genome-resolved surveillance and predictive ecological risk modeling of urban microbiomes.Microbiome · 2025Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model.mSystems · 2023Article
- MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues.Journal of molecular biology · 2023Article
- Contamination detection and microbiome exploration with GRIMER.GigaScience · 2022Article
- Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.Microorganisms · 2022Review
- Constructing metagenome-assembled genomes for almost all components in a real bacterial consortium for binning benchmarking.BMC genomics · 2022Article
- The Notable Achievements and the Prospects of Bacterial Pathogen Genomics.Microorganisms · 2022Article
- BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies.Communications biology · 2022Article
- Genome-Resolved Characterization of Structure and Potential Functions of the Zebrafish Stool Microbiome.Frontiers in cellular and infection microbiology · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels.Frontiers in microbiology · 2022Review
- A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data.Computational and structural biotechnology journal · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.
Indexed as
Identifiers
What OpenQuestion holds
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.