Table 1.
Core modules and integrated tools of ViroProfiler.
| Software | Module | License | Reference |
|---|---|---|---|
| metaSPAdes | Assembly | NA | 35 |
| vRhyme | Binning | GPL v3 | 36 |
| Phamb | Binning | MIT | 37 |
| CheckV | Virus detection and QC | BSD | 20 |
| VirSorter2 | Virus detection | GPL v2 | 9 |
| DeepVirFinder | Virus detection | USC-RL v1.0 | 11 |
| VIBRANT | Virus detection and gene annotation | GPL v3 | 10 |
| DRAM | Functional annotation | GPL v3 | 21 |
| eggnog-mapper | Functional annotation | GPL v3 | 22,23 |
| abricate | Functional annotation | GPL v2 | https://github.com/tseemann/abricate |
| MMseqs2 | Taxonomy assignment | GPL v3 | 24 |
| vConTACT2 | Taxonomy assignment | GPL v3 | 18 |
| Bacphlip | Replication cycle prediction | MIT | 26 |
| Replidec | Replication cycle prediction | MIT | 27 |
| iPHoP | Host prediction | GPL v3 | 25 |
| CoverM | Abundance estimation | GPL v3 | https://github.com/wwood/CoverM |
| Kraken2 | Virus detection | MIT | 30 |
| Bracken | Abundance estimation | GPL v3 | 31 |