Fast and robust metagenomic sequence comparison through sparse chaining with skani.

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.

SUBMITTER: Shaw J 

PROVIDER: S-EPMC10630134 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature