SeqDesk · original analysis
Citation adoption for curated functional & pathway annotation tools, counted weekly from OpenAlex.
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
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 7 curated tools with a datable code repository (0 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 functional & pathway annotation tool is recomputed for each complete calendar year by cumulative citations — a 1-way hand-off across 12 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 |
|---|---|---|---|---|---|---|---|
| InterProScan 5 | Functional & pathway annotation | 9,317 | 2025 (1.3K/yr) | GitHub ↗ | 385 | this month | active |
| PICRUSt2 | Functional & pathway annotation | 6,736 | 2025 (1.5K/yr) | GitHub ↗ | 392 | 7 mo ago | active |
| eggNOG-mapper v2 | Functional & pathway annotation | 5,273 | 2025 (1.5K/yr) | GitHub ↗ | 749 | 1 mo ago | active |
| HUMAnN 3 | Functional & pathway annotation | 2,287 | 2025 (549/yr) | GitHub ↗ | 247 | this month | active |
| dbCAN2 | Functional & pathway annotation | 2,284 | 2023 (437/yr) | GitHub ↗ | 166 | 1.2 yr ago | active |
| KofamScan | Functional & pathway annotation | 2,032 | 2025 (419/yr) | GitHub ↗ | 100 | 3.1 yr ago | stale |
| DRAM | Functional & pathway annotation | 1,133 | 2025 (297/yr) | GitHub ↗ | 333 | this month | active |
A curated cohort of functional & pathway annotation 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