SeqDesk · original analysis
Citation adoption for curated plasmid recovery & typing 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 14 curated tools with a datable code repository (1 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 plasmid recovery & typing tool is recomputed for each complete calendar year by cumulative citations — a 2-way hand-off across 14 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 |
|---|---|---|---|---|---|---|---|
| PlasmidFinder | Plasmid recovery & typing | 4,885 | 2025 (665/yr) | GitHub ↗ | 32 | 2.7 yr ago | stale |
| MOB-suite | Plasmid recovery & typing | 977 | 2025 (269/yr) | GitHub ↗ | 177 | 1.2 yr ago | active |
| PlasFlow | Plasmid recovery & typing | 635 | 2025 (108/yr) | GitHub ↗ | 111 | 5.0 yr ago | stale |
| plasmidSPAdes | Plasmid recovery & typing | 555 | 2021 (83/yr) | GitHub ↗ | 947 | this month | active |
| Platon | Plasmid recovery & typing | 219 | 2025 (50/yr) | GitHub ↗ | 122 | 1 mo ago | active |
| PPR-Meta | Plasmid recovery & typing | 198 | 2023 (41/yr) | GitHub ↗ | 44 | 5.2 yr ago | stale |
| Recycler | Plasmid recovery & typing | 159 | 2021 (28/yr) | GitHub ↗ | 58 | 5.2 yr ago | stale |
| PlasClass | Plasmid recovery & typing | 140 | 2025 (29/yr) | GitHub ↗ | 33 | 2.0 yr ago | stale |
| COPLA | Plasmid recovery & typing | 132 | 2023 (38/yr) | GitHub ↗ | 28 | 5.0 yr ago | stale |
| cBar | Plasmid recovery & typing | 124 | 2020 (24/yr) | web ↗ | — | — | unknown |
| PLASMe | Plasmid recovery & typing | 91 | 2025 (50/yr) | GitHub ↗ | 35 | 2.2 yr ago | stale |
| SCAPP | Plasmid recovery & typing | 71 | 2023 (17/yr) | GitHub ↗ | 37 | 3.3 yr ago | stale |
| Deeplasmid | Plasmid recovery & typing | 57 | 2024 (18/yr) | GitHub ↗ | 21 | 1.8 yr ago | stale |
| Plasmer | Plasmid recovery & typing | 52 | 2024 (19/yr) | GitHub ↗ | 50 | 3.2 yr ago | stale |
| gplas | Plasmid recovery & typing | 37 | 2022 (9/yr) | GitLab ↗ | 4 | 3.2 yr ago | stale |
A curated cohort of plasmid recovery & typing 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