Fast and robust metagenomic sequence comparison through sparse chaining with skani.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 37735570.
- Also identified by DOI 10.1038/s41592-023-02018-3 and PMC identifier 10630134.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Metagenome
- Prokaryotic Cells