SeqDesk · original analysis
Citation adoption for curated strain-level resolution 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 6 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 2026-06-25.
The leading strain-level resolution tool is recomputed for each complete calendar year by cumulative citations — a 2-way hand-off across 10 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 |
|---|---|---|---|---|---|---|---|
| StrainPhlAn | Strain-level resolution | 951 | 2021 (116/yr) | GitHub ↗ | 413 | this month | active |
| inStrain | Strain-level resolution | 585 | 2025 (145/yr) | GitHub ↗ | 190 | 4 mo ago | active |
| MIDAS | Strain-level resolution | 531 | 2022 (88/yr) | GitHub ↗ | 135 | 2.7 yr ago | stale |
| DESMAN | Strain-level resolution | 221 | 2021 (45/yr) | GitHub ↗ | 72 | 6.0 yr ago | stale |
| StrainGE | Strain-level resolution | 109 | 2025 (40/yr) | GitHub ↗ | 41 | 1.7 yr ago | stale |
| Strainberry | Strain-level resolution | 67 | 2024 (16/yr) | GitHub ↗ | 52 | 4.6 yr ago | stale |
A curated cohort of strain-level resolution 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