Fast and robust metagenomic sequence comparison through sparse chaining with skani

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.

• CN
  Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada

  Award: RGPIN-2022-03074
• NS
  Natural Sciences and Engineering Research Council of Canada

  Awards: DGDND-2022-03074, RGPIN-2022-03074