ReviewComputational and structural biotechnology journal2021
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data.
Review in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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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.
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Who cites it
110 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.Molecular biology reports · 2025Pooled it
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- DecBin: Bayesian-optimized deep clustering for long-read metagenomic binning.Briefings in bioinformatics · 2026Article
- Environmental filtering shapes biosynthetic potential and resistome of antarctic microbiomes.World journal of microbiology & biotechnology · 2026Article
- WASP: a pipeline for functional annotation prediction based on AlphaFold structural models.Nature communications · 2026Article
- Taxonomy bias in metagenome-assembled genome recovery.Microbial genomics · 2026Article
- StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.Bioinformatics (Oxford, England) · 2026Article
- Benchmarking shotgun metagenomics.Nature microbiology · 2026Article
- Article
- 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
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Proof-of-concept of host attribution of antimicrobial resistance genes using wastewater Hi-C metagenome sequencing.Journal of water and health · 2026Article
- gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research.Nucleic acids research · 2026Article
- Article
- Identifying Differential Network Properties and Driver Microbes in Microbial Association Networks Using CompNet and NetShift.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Microbiome Profiling in Chagas Disease: Sample Collection, Sequencing, and Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Annotation of glycoside hydrolases in unassembled metagenomes using CAZyOBioinformatics advances · 2026Article
- Review
- Advances and Hotspots in Research on Verrucomicrobiota: Focus on Agroecosystems.Microbial ecology · 2025Review
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
50 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomic sequencing provides a culture-independent avenue to investigate the complex microbial communities by constructing metagenome-assembled genomes (MAGs). A MAG represents a microbial genome by a group of sequences from genome assembly with similar characteristics. It enables us to identify novel species and understand their potential functions in a dynamic ecosystem. Many computational tools have been developed to construct and annotate MAGs from metagenomic sequencing, however, there is a prominent gap to comprehensively introduce their background and practical performance. In this paper, we have thoroughly investigated the computational tools designed for both upstream and downstream analyses, including metagenome assembly, metagenome binning, gene prediction, functional annotation, taxonomic classification, and profiling. We have categorized the commonly used tools into unique groups based on their functional background and introduced the underlying core algorithms and associated information to demonstrate a comparative outlook. Furthermore, we have emphasized the computational requisition and offered guidance to the users to select the most efficient tools. Finally, we have indicated current limitations, potential solutions, and future perspectives for further improving the tools of MAG construction and annotation. We believe that our work provides a consolidated resource for the current stage of MAG studies and shed light on the future development of more effective MAG analysis tools on metagenomic sequencing.
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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.