Fast and robust metagenomic sequence comparison through sparse chaining with skani

Shaw, J.; Yu, Y. W.

doi:10.1101/2023.01.18.524587

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bioRxiv · 10.1101/2023.01.18.524587

Fast and robust metagenomic sequence comparison through sparse chaining with skani

Shaw, J.·Yu, Y. W.

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Abstract

Sequence comparison algorithms for metagenome-assembled genomes (MAGs) often have difficulties dealing with data that is high-volume or low-quality. We present skani (https://github.com/bluenote-1577/skani), a method for calculating average nucleotide identity (ANI) using sparse approximate alignments. skani is more accurate than FastANI for comparing incomplete, fragmented MAGs while also being > 20 times faster. For searching a database of > 65, 000 prokaryotic genomes, skani takes only seconds per query and 6 GB of memory. skani is a versatile tool that unlocks higher-resolution insights for larger, noisier metagenomic data sets.

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Shaw, J., Yu, Y. W.. 2023-01-20. Fast and robust metagenomic sequence comparison through sparse chaining with skani. https://doi.org/10.1101/2023.01.18.524587

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