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cff-version: 1.2.0
title: Pyskani
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Martin
    family-names: Larralde
    email: martin.larralde@embl.de
    affiliation: Leiden University Medical Center
    orcid: 'https://orcid.org/0000-0002-3947-4444'
  - given-names: Georg
    family-names: Zeller
    affiliation: Leiden University Medical Center
    orcid: 'https://orcid.org/0000-0003-1429-7485'
  - given-names: Laura
    name-particle: M.
    family-names: Carroll
    affiliation: Umeå University
    orcid: 'https://orcid.org/0000-0002-3677-0192'
identifiers:
  - type: doi
    value: 10.1101/2025.02.13.638148
    description: bioRxiv preprint
  - type: doi
    value: 10.1093/nargab/lqaf095
    description: NAR Genomics & Bioinformatics paper
repository-code: 'https://github.com/althonos/pyskani'
abstract: >-
  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.
keywords:
  - python
  - library
  - average nucleotide identity
  - ANI
license: MIT
preferred-citation:
  type: article
  authors:
  - given-names: Martin
    family-names: Larralde
    email: martin.larralde@embl.de
    affiliation: Leiden University Medical Center
    orcid: 'https://orcid.org/0000-0002-3947-4444'
  - given-names: Georg
    family-names: Zeller
    affiliation: Leiden University Medical Center
    orcid: 'https://orcid.org/0000-0003-1429-7485'
  - given-names: Laura
    name-particle: M.
    family-names: Carroll
    affiliation: Umeå University
    orcid: 'https://orcid.org/0000-0002-3677-0192'
  doi: "10.1093/nargab/lqaf095"
  journal: "NAR Genomics and Bioinformatics"
  volume: 7
  issue: 3
  title: "PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity"
  year: 2025
  month: 9
