| name | skani |
| description | Fast robust average nucleotide identity (ANI) for metagenomic genomes and MAG comparisons. Use for species-level clustering, novelty vs GTDB/UHGG, and scalable ANI matrices. Upstream: https://github.com/bluenote-1577/skani.
|
| license | MIT |
| category | analysis-tools |
| tags | ["ANI","comparative-genomics","MAG"] |
| upstream | https://github.com/bluenote-1577/skani |
| stage | binning |
skani
Upstream: bluenote-1577/skani
Citation
Shaw, J. & Yu, Y. W. Fast and robust metagenomic sequence comparison through
sparse chaining with skani. Nat. Methods 20, 1661–1665 (2023).
https://doi.org/10.1038/s41592-023-02018-3
Analytical thinking
skani estimates ANI quickly on incomplete MAGs better than many classic
tools that assume near-complete genomes. Use for:
- Dereplication cross-checks vs
drep · fastani
- Novelty vs GTDB reps / UHGG (
mgnify)
- All-vs-all MAG similarity heatmaps
95% ANI remains a common species-level heuristic — state your cutoff.
vs FastANI
| skani | fastani |
|---|
| Strength | Speed/robustness on incomplete MAGs; large catalogues | Classic literature-compatible ANI |
| Prefer | New large MAG studies | Reproducing FastANI-based Methods |
| Skill | this | fastani |
Do not mix FastANI and skani values in one unlabeled matrix.
How to run
conda install -c bioconda skani
skani triangle bins_hq/*.fa > temp/ani/skani.triangle
skani dist bins_hq/query.fa bins_hq/*.fa > temp/ani/query_vs_all.tsv
Related skills
fastani · drep · gtdb · mgnify · checkm2 · gtdbtk · mag-qc
