SeqDesk · original analysis
Citation adoption for curated taxonomic profiling & classification 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 22 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 taxonomic profiling & classification 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 |
|---|---|---|---|---|---|---|---|
| DIAMOND | Taxonomic profiling & classification | 14,127 | 2025 (2.1K/yr) | GitHub ↗ | 1.3K | this month | active |
| Kraken 2 | Taxonomic profiling & classification | 7,091 | 2025 (1.5K/yr) | GitHub ↗ | 916 | this month | active |
| GTDB-Tk | Taxonomic profiling & classification | 5,274 | 2025 (980/yr) | GitHub ↗ | 609 | 1 mo ago | active |
| Kraken | Taxonomic profiling & classification | 4,501 | 2020 (523/yr) | GitHub ↗ | 226 | 4.8 yr ago | stale |
| Bracken | Taxonomic profiling & classification | 2,308 | 2025 (492/yr) | GitHub ↗ | 354 | 4 mo ago | active |
| MetaPhlAn2 | Taxonomic profiling & classification | 2,180 | 2021 (336/yr) | GitHub ↗ | 413 | this month | active |
| Kaiju | Taxonomic profiling & classification | 2,121 | 2024 (297/yr) | GitHub ↗ | 303 | this month | active |
| MetaPhlAn | Taxonomic profiling & classification | 1,773 | 2021 (206/yr) | GitHub ↗ | 413 | this month | active |
| MEGAN CE | Taxonomic profiling & classification | 1,756 | 2021 (231/yr) | GitHub ↗ | 75 | 2.0 yr ago | stale |
| Centrifuge | Taxonomic profiling & classification | 1,432 | 2024 (188/yr) | GitHub ↗ | 275 | 3 mo ago | active |
| MetaPhlAn 4 | Taxonomic profiling & classification | 1,424 | 2025 (518/yr) | GitHub ↗ | 413 | this month | active |
| CLARK | Taxonomic profiling & classification | 632 | 2019 (75/yr) | GitHub ↗ | 2 | this month | active |
| PhyloSift | Taxonomic profiling & classification | 631 | 2017 (88/yr) | GitHub ↗ | 82 | 10 yr ago | stale |
| CAT/BAT | Taxonomic profiling & classification | 543 | 2024 (95/yr) | GitHub ↗ | 231 | 3 mo ago | active |
| KrakenUniq | Taxonomic profiling & classification | 476 | 2025 (80/yr) | GitHub ↗ | 252 | 2.4 yr ago | stale |
| mOTUs2 | Taxonomic profiling & classification | 445 | 2022 (96/yr) | GitHub ↗ | 177 | this month | active |
| sourmash | Taxonomic profiling & classification | 329 | 2025 (53/yr) | GitHub ↗ | 548 | this month | active |
| MMseqs2 taxonomy | Taxonomic profiling & classification | 312 | 2025 (75/yr) | GitHub ↗ | 2.1K | this month | active |
| sylph | Taxonomic profiling & classification | 109 | 2026 (54/yr) | GitHub ↗ | 312 | 5 mo ago | active |
| ganon | Taxonomic profiling & classification | 73 | 2022 (15/yr) | GitHub ↗ | 106 | this month | active |
| Metabuli | Taxonomic profiling & classification | 41 | 2025 (20/yr) | GitHub ↗ | 179 | 3 mo ago | active |
| Centrifuger | Taxonomic profiling & classification | 38 | 2026 (18/yr) | GitHub ↗ | 92 | this month | active |
A curated cohort of taxonomic profiling & classification 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