Fast and robust metagenomic sequence comparison through sparse chaining with skani
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Updated: Jul 16, 2025

Metagenomic Analysis of Silage
Published on: January 13, 2017
Jim Shaw1, Yun William Yu2,3,4
1Department of Mathematics, University of Toronto, Toronto, Ontario, Canada. jshaw@math.toronto.edu.
Abstract:
Sequence comparison tools for metagenome-assembled genomes (MAGs) struggle with high-volume or low-quality data. We present skani ( https://github.com/bluenote-1577/skani ), a method for determining average nucleotide identity (ANI) via sparse approximate alignments. skani outperforms FastANI in accuracy and speed (>20× faster) for fragmented, incomplete MAGs. skani can query genomes against >65,000 prokaryotic genomes in seconds and 6 GB memory. skani unlocks higher-resolution insights for extensive, noisy metagenomic datasets.
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