| name | sylph |
| description | Rapid species-level metagenome profiling and containment estimation. Use this skill when working with sylph: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/bluenote-1577/sylph. For stage routing use tool-selection / metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["taxonomy","sketch","profile"] |
| upstream | https://github.com/bluenote-1577/sylph |
| stage | taxonomy |
sylph
Upstream: sylph
Citation
Shaw, J. & Yu, Y. W. Rapid species-level metagenome profiling and containment estimation with sylph. Nat. Biotechnol. 43, 1348–1359 (2025). https://doi.org/10.1038/s41587-024-02412-y
See also docs/references.md.
Analytical thinking
Containment ANI between a reference genome and a metagenome is biased at low
coverage (missing k-mers look like divergence). Sylph models k-mer coverage
with a zero-inflated Poisson, estimates effective coverage λ, and reports
coverage-adjusted ANI plus abundances — two orthogonal outputs.
Why it matters:
- Very fast sketch-based profiling for large cohorts / large genome databases.
- Better presence/ANI calls for low-coverage genomes than naive containment.
- Complementary to MetaPhlAn (markers) and Kraken (LCA k-mers); cite sketch DB.
- User coverage thresholds still matter; assembly incompleteness ≠ low coverage.
How to run
conda install -c bioconda sylph
sylph sketch -c 200 reads_1.fq.gz reads_2.fq.gz -o temp/sylph/${id}
sylph profile temp/sylph/${id}.syldb database.syldb -o temp/sylph/${id}.tsv
Key parameters
| Parameter | Notes |
|---|
-c | Subsampling rate (default 200 in paper examples) |
| sketch DB | Prebuilt (e.g. GTDB-based) or custom — pin version |
| coverage threshold | Presence gate; report in Methods |
profile vs query | Abundance profiling vs genome containment ANI |
Decision notes
- Stage: taxonomy / genome presence
- Prefer for large-scale genome-resolved containment + profiling speed
- Do not merge with MetaPhlAn/Kraken unlabeled
Related skills
metaphlan · kraken2 · motus · metabuli · skani · coverm ·
tool-selection · metagenomics-workflow
