fastani

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
# or --ql / --rl lists for many genomes

Related skills

skani · drep · gtdb · mgnify · coverm · tool-selection