| name | fastani |
| description | FastANI — alignment-free approximate mapping for high-throughput average nucleotide identity (ANI) among prokaryotic genomes/MAGs. Use when: (1) Reproducing literature that reports FastANI, (2) Pairwise/species-boundary ANI at moderate catalogue scales, (3) Comparing to skani for Methods. Upstream: https://github.com/ParBLiSS/FastANI. Prefer skani for very large MAG sets / incomplete genomes unless FastANI is required for compatibility.
|
| license | MIT |
| category | analysis-tools |
| tags | ["ANI","FastANI","comparative-genomics"] |
| upstream | https://github.com/ParBLiSS/FastANI |
| stage | binning |
FastANI
Upstream: ParBLiSS/FastANI
Citation
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S.
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species
boundaries. Nat. Commun. 9, 5114 (2018).
https://doi.org/10.1038/s41467-018-07641-9
See also docs/references.md.
Analytical thinking
FastANI popularized scalable ~95% ANI species-boundary analyses. Still widely
cited in Methods even when newer tools are faster.
| Tool | Prefer when |
|---|
skani | Large MAG catalogues; incomplete MAGs; speed/memory |
fastani | Compatibility with published FastANI thresholds / pipelines |
drep | Dereplication workflow (may call ANI backends) |
State the ANI tool + version + cutoff (commonly 95% species; AF/alignment
fraction matters — report it).
How to run
conda install -c bioconda fastani
fastani -q query.fa -r reference.fa -o temp/fastani/out.txt
Related skills
skani · drep · gtdb · mgnify · coverm · tool-selection
