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Skani enables accurate and efficient genome comparison for modern metagenomic datasets

Nature Methods volume 20, pages 1633–1634 (2023)Cite this article

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Modern high-throughput metagenomics is producing hundreds of thousands of metagenome-assembled genomes (MAGs), which is overwhelming traditional sequence-similarity search methods. We present a computational method, skani, that efficiently compares MAGs on a terabyte scale while being robust to the inherent noise in MAGs, enabling larger and more accurate analyses.

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Fig. 1: Skani gives improved clustering and speed over competing methods.

References

  1. Nayfach, S. et al. A genomic catalog of Earth’s microbiomes. Nat. Biotechnol. 39, 499–509 (2021). This paper highlights the scale of modern collections of MAGs, which number in the hundreds of thousands.

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  2. Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016). This paper reports one of the first sketching methods for the rapid analysis of genomes.

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  5. Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017). This paper shows that Mash gives incorrect estimates of ANI in the presence of MAG incompleteness.

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This is a summary of: Shaw, J. & Yu, Y. W. Fast and robust metagenomic sequence comparison through sparse chaining with skani. Nat. Methods, https://doi.org/10.1038/s41592-023-02018-3 (2023).

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Skani enables accurate and efficient genome comparison for modern metagenomic datasets. Nat Methods 20, 1633–1634 (2023). https://doi.org/10.1038/s41592-023-02019-2

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