skani ☆
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Description:
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics metagenomics ani sequence-alignment
Install: brew install skani
About:
Skani is a fast and robust tool for computing Average Nucleotide Identity (ANI) and aligned fraction between genomes, specifically optimized for metagenomic contigs and fragmented assemblies. Unlike traditional tools, it uses a sparse seed-and-extend approach that is highly accurate and memory-efficient on incomplete or low-quality data. This makes it ideal for large-scale comparative genomics and metagenomic binning validation.
Key Features:
  • Optimized for fragmented metagenomic contigs
  • Fast sparse seed-and-extend algorithm
  • Low memory footprint
  • Robust to assembly fragmentation
Use Cases:
  • Validating metagenomic bin quality
  • Comparative genomics of microbial isolates
  • Taxonomic classification via ANI
Alternatives:
  • FastANI – FastANI is faster on complete genomes but less accurate on fragmented contigs.
  • MUMmer – MUMmer is more accurate but significantly slower and memory-intensive for large datasets.
Version History
Detected Version Rev Change Commit
Sep 14, 2025 4:38am 0 VERSION_BUMP 635e5cfa
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