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bioRxiv · 10.64898/2026.11.05.764740

Homology-aware average nucleotide identity estimation at scale with TurboANI

Zhao, J.·McDonald, D.·Patel, L.·Wang, C.·Gonzalez, A.·Knight, R.
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Abstract

Here we introduce TurboANI, a fast homology-aware average nucleotide identity (ANI) estimation algorithm that implements the seed-chain-quasi-alignment scheme using SIMD seeding, compact indexing, lightweight chaining, and cache-friendly bitset sliding minwise hashing, achieving up to ~40,000-fold speedup over the alignment-based ANI algorithm with near-perfect agreement. TurboANI is also >40-fold faster than the state-of-the-art FastANI and ten-fold faster than skani while maintaining better accuracy. In the sensitive mode, it has a ten-fold higher true-ANI recovery rate than skani.

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Zhao, J., McDonald, D., Patel, L., Wang, C., Gonzalez, A., Knight, R.. 2026-11-09. Homology-aware average nucleotide identity estimation at scale with TurboANI. https://doi.org/10.64898/2026.11.05.764740

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