Install skani with Homebrew

Project links

• Homepage
• Package manager page

Commands and aliases

• skani

Project history

skani was developed by Jim Shaw with Yun William Yu to calculate average nucleotide identity and aligned fraction through sparse chaining without base-level alignment. The method was described in Nature Methods in 2023.

Subsequent releases expanded and refined database searching, memory use, command-line behavior, and output controls. The project maintains detailed usage guides and tutorials in its official GitHub wiki.

Adoption history

The project is distributed through source builds, release binaries, Conda/Bioconda, and Homebrew. Its official README also points users to independent Rust and Python interfaces, indicating use both as a command-line program and as a component in bioinformatics workflows.

How it is used

Common operations include pairwise genome comparison with `skani dist`, database construction with `skani sketch`, database querying with `skani search`, and all-versus-all matrix or edge-list generation with `skani triangle`.

The tool is aimed primarily at comparisons above roughly 80% ANI. Its documentation warns that default filtering may produce no output when aligned fraction is too low.

Why package nerds care

skani is notable to scientific-package users because it combines a Rust implementation with a specialized genomics algorithm, preprocessed searchable databases, multithreaded CLI operations, and reproducible package-manager distribution. It occupies the performance-oriented space between sketching tools such as Mash and alignment-based ANI programs such as FastANI.

Timeline

• 2023: The skani method was described by Jim Shaw and Yun William Yu in Nature Methods.
• 2025: Version 0.3.0 introduced a consolidated searchable database format and reduced memory consumption, with command-line changes documented as breaking.
• 2025: The official wiki was updated with expanded usage guides, tutorials, and database workflows.

Related projects

• Mash: a genome-distance sketching tool discussed by skani's documentation as a faster but potentially less accurate comparator for incomplete MAGs.
• FastANI: an ANI implementation used as a performance and accuracy comparator in the skani project.
• pyskani: independent Python bindings referenced by the official skani README.
• skani-lib-example: an official minimal example for embedding skani as a Rust library.

Sources

• Official skani releases: https://github.com/bluenote-1577/skani/releases
• Official skani repository README: https://github.com/bluenote-1577/skani#readme
• Official skani wiki: https://github.com/bluenote-1577/skani/wiki