Table 1. Comparison of MicrobiomeAnalyst with other web-based tools. The URL for each tool is given below the table. Tools dedicated solely for sequence annotation are not included.
| Tools | Microbiome-Analyst | METAGEN-assist | EBI-Metagenomics | MG-RAST | VAMPS |
|---|---|---|---|---|---|
| Registration | No | No | Yes | Yes | Yes |
| Data Processing | |||||
| Input | Count tables; BIOM; mothur output | Count tables; BIOM; outputs from 4 tools | Sequences | Sequences | Sequences |
| Filtering | Abundance, variance, manual | Abundance, variance | – | Abundance | Abundance |
| Normalization | Scaling, transformation, rarefying | Scaling, transformation | – | Scaling, trans-formation | Scaling |
| Taxonomic Profiling | |||||
| Alpha-diversity | Multiple | – | – | Shannon | Multiple |
| Beta-diversity | PCoA & NMDS (2D & 3D) | PCA, PLS-DA | PCA | PCoA | PCoA & NMDS (2D only) |
| Functional profiling | |||||
| Functional prediction | PICRUSt & Tax4Fun | – | – | – | – |
| Functional annotation | COG & KEGG | – | GO | SEED, KEGG COG, eggNOG | – |
| Pathway visualization | Yes (JavaScript) | – | – | Yes (SVG) | – |
| Comparative analysis | |||||
| Differential analysis | Univariate methods, DESeq2, edgeR, metagenomeSeq | Univariate methods | – | – | – |
| Biomarker discovery & classification | LEfSe, Random Forests | SVM, Random Forests | – | – | – |
| Meta-analysis | |||||
| Taxon set enrichment analysis | 105 strain sets, 174 species sets, 42 others | – | – | – | – |
| Integration with public data | Visual analytics with 3D PCoA | – | – | – | – |
• MicrobiomeAnalyst: http://www.microbiomeanalyst.ca/
• METAGENassist: http://www.metagenassist.ca/
• EBI-Metagenomics: https://www.ebi.ac.uk/metagenomics/
• MG-RAST: http://metagenomics.anl.gov/
• VAMPS: https://vamps2.mbl.edu/