SeqDesk · original analysis
Citation adoption for curated metagenome assembly 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 11 curated tools with a datable code repository (2 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 metagenome assembly tool is recomputed for each complete calendar year by cumulative citations — a 3-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 |
|---|---|---|---|---|---|---|---|
| SPAdes | Metagenome assembly | 27,175 | 2021 (3.4K/yr) | GitHub ↗ | 947 | this month | active |
| MEGAHIT | Metagenome assembly | 9,944 | 2025 (2.0K/yr) | GitHub ↗ | 719 | 8 mo ago | active |
| Unicycler | Metagenome assembly | 8,768 | 2025 (1.5K/yr) | GitHub ↗ | 645 | 1.9 yr ago | stale |
| Canu | Metagenome assembly | 8,170 | 2021 (1.1K/yr) | GitHub ↗ | 701 | this month | active |
| Flye | Metagenome assembly | 6,324 | 2025 (1.4K/yr) | GitHub ↗ | 941 | 3 mo ago | active |
| metaSPAdes | Metagenome assembly | 4,817 | 2024 (741/yr) | GitHub ↗ | 947 | this month | active |
| IDBA-UD | Metagenome assembly | 3,226 | 2022 (337/yr) | GitHub ↗ | 132 | 3.0 yr ago | stale |
| metaFlye | Metagenome assembly | 1,126 | 2025 (272/yr) | GitHub ↗ | 941 | 3 mo ago | active |
| MetaVelvet | Metagenome assembly | 692 | 2015 (83/yr) | GitHub ↗ | 15 | 14 yr ago | stale |
| Ray Meta | Metagenome assembly | 620 | 2017 (88/yr) | GitHub ↗ | 68 | 8.9 yr ago | stale |
| OPERA-MS | Metagenome assembly | 433 | 2024 (73/yr) | GitHub ↗ | 102 | 2.0 yr ago | stale |
| MOCAT | Metagenome assembly | 210 | 2016 (39/yr) | web ↗ | — | — | stale |
| MetaHipMer | Metagenome assembly | 76 | 2025 (21/yr) | Bitbucket ↗ | — | — | stale |
A curated cohort of metagenome assembly 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