PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity
bioRxiv – February 13, 2025
Source: medRxiv/bioRxiv/arXiv
Summary
Average nucleotide identity (ANI) is essential for identifying prokaryotic species in genomics. New Python libraries—PyOrthoANI, PyFastANI, and Pyskani—simplify ANI calculations, producing results consistent with established methods. They integrate smoothly with BioPython, enhancing bioinformatic workflows and making genomic analysis more accessible.
Abstract
Summary The average nucleotide identity (ANI) metric has become the gold standard for prokaryotic species delineation in the genomics era. The most popular ANI algorithms are available as command-line tools and/or web applications, making it inconvenient or impossible to incorporate them into bioinformatic workflows, which utilize the popular Python programming language. Here, we present PyOrthoANI, PyFastANI, and Pyskani, Python libraries for three popular ANI computation methods. ANI values produced by PyOrthoANI, PyFastANI, and Pyskani are virtually identical to those produced by OrthoANI, FastANI, and skani, respectively. All three libraries integrate seamlessly with BioPython, making it easy and convenient to use, compare, and benchmark popular ANI algorithms within Python-based workflows.