SeqDesk · original analysis
Citation adoption for curated viral discovery & viromics tools, counted weekly from OpenAlex.
Use cumulative view for long-run adoption and annual view for citation momentum; log scale makes smaller tools readable without changing the counts. Counts are annual OpenAlex cited-by tallies and reflect all uses of each paper, not only use inside the selected workflow; broad tools can therefore look larger than workflow-specific methods. The still-filling current year (2026) is omitted from the lines.
Each dot is one of 11 curated tools with a datable code repository (4 web-only / SourceForge tools without a public commit date aren't shown). Higher means more cited in 2025, the latest complete year (log scale); further left means more recently updated (square-root scale). Filled dots are actively maintained — a commit within the last 18 months. The upper-left gathers the field's well-kept, widely-used staples: fastp, SAMtools, DADA2, SPAdes, Prokka, DIAMOND and more, updated regularly and cited thousands of times a year. Maintenance and citations are only loosely linked (Spearman ρ ≈ −0.46): a citation counts every paper that mentions a method, so a quieter commit history does not mean a tool is unused or unmaintained — many stable, widely-relied-on tools rarely need new commits, and development sometimes moves to mirrors this snapshot can't see. Source: OpenAlex citation graph + GitHub/GitLab activity, as of 2026-10-19.
The leading viral discovery & viromics tool is recomputed for each complete calendar year by cumulative citations — a 2-way hand-off across 11 years.
cites: grouped by year when available; counts_by_year fallback when the grouped endpoint is budget-limited)scripts/check-tool-trends.mjs| Tool | Group | Lifetime citations | Peak year | Source | Stars | Last commit | Status |
|---|---|---|---|---|---|---|---|
| PHASTER | Viral discovery & viromics | 3,561 | 2021 (527/yr) | web ↗ | — | — | unknown |
| CheckV | Viral discovery & viromics | 1,760 | 2025 (447/yr) | Bitbucket ↗ | — | — | stale |
| VirSorter2 | Viral discovery & viromics | 1,283 | 2025 (329/yr) | GitHub ↗ | 293 | 1.6 yr ago | stale |
| VIBRANT | Viral discovery & viromics | 1,127 | 2025 (244/yr) | GitHub ↗ | 197 | 2.2 yr ago | stale |
| VirSorter | Viral discovery & viromics | 1,106 | 2021 (180/yr) | GitHub ↗ | 101 | 5.7 yr ago | stale |
| geNomad | Viral discovery & viromics | 1,019 | 2026 (445/yr) | GitHub ↗ | 318 | 3 mo ago | active |
| vConTACT2 | Viral discovery & viromics | 946 | 2024 (169/yr) | Bitbucket ↗ | — | — | stale |
| DeepVirFinder | Viral discovery & viromics | 659 | 2025 (141/yr) | GitHub ↗ | 154 | 2 mo ago | active |
| VirFinder | Viral discovery & viromics | 646 | 2024 (90/yr) | GitHub ↗ | 138 | 6.2 yr ago | stale |
| iPHoP | Viral discovery & viromics | 468 | 2025 (166/yr) | Bitbucket ↗ | — | — | stale |
| PhaTYP | Viral discovery & viromics | 228 | 2026 (75/yr) | GitHub ↗ | 19 | 1.6 yr ago | stale |
| MARVEL | Viral discovery & viromics | 163 | 2021 (32/yr) | GitHub ↗ | 51 | 2.2 yr ago | stale |
| Cenote-Taker 2 | Viral discovery & viromics | 146 | 2024 (36/yr) | GitHub ↗ | 56 | 2.4 yr ago | stale |
| Seeker | Viral discovery & viromics | 135 | 2022 (27/yr) | GitHub ↗ | 33 | 5.0 yr ago | stale |
| PhaGCN2 | Viral discovery & viromics | 133 | 2025 (43/yr) | GitHub ↗ | 35 | 1.0 yr ago | active |
A curated cohort of viral discovery & viromics tools, each tracked by the full citation history of its method paper — re-counted weekly straight from the OpenAlex citation graph. Only the published method papers and their public citation counts are used. · show all tool groups · back to all research data