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Updated: Jan 23, 2026
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Metagenomic Analysis of Silage
Published on: January 13, 2017
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A comprehensive comparison of web-based tools for amplicon-metagenomic analysis
Yuhe Kan1, Xiao-Yu Ma2, Yi-Lu Wang2
1College of Biology and Oceanography, Weifang University, Weifang, Shandong, China.
Frontiers in Microbiology
|January 22, 2026
Summary
This review systematically evaluated eight web-based microbiome analysis tools for users without scripting experience. MicrobiomeAnalyst 2.0, Mian, and Namco demonstrated the highest overall performance, aiding researchers in selecting appropriate microbiome profiling tools.
Area of Science:
- Microbiome research
- Bioinformatics
- Computational biology
Background:
- Amplicon sequencing is a key method for microbiome profiling.
- Numerous R-based and web-based tools exist for microbiome data analysis.
- There is a need for systematic evaluation of user-friendly web-based tools.
Purpose of the Study:
- To systematically evaluate eight freely accessible web-based tools for microbiome profiling.
- To compare tool performance across various analytical modules.
- To provide a practical reference for researchers selecting microbiome analysis software.
Main Methods:
- Comparative analysis of eight web-based microbiome analysis tools.
- Evaluation across modules: diversity, composition, differential analysis, network analysis, functional profiling, machine learning, and visualization.
- Assessment of user experience and tool limitations.
Main Results:
- MicrobiomeAnalyst 2.0, Mian, and Namco showed the highest overall performance.
- Specific tools excelled in particular modules: MicrobiomeAnalyst 2.0 (differential comparison, functional analysis), Mian (alpha diversity, taxonomic composition), METAGENassist (beta diversity), Namco (network analysis).
- Limitations include inconsistent accessibility, diverse data formats, and restricted features.
Conclusions:
- MicrobiomeAnalyst 2.0 is the top-performing tool, followed by Mian and Namco.
- Future tool development should focus on preprocessing, interactive visualization, advanced statistics, and multi-omics integration.
- This assessment guides researchers in choosing suitable web-based tools for microbiome analysis.
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