To cite strainspy in publications, please use:

Mallawaarachchi S, Tandon K, Rajan N, Marcelino V, Sandhu S, Bedoui S, Ingle D, Gunjur A, Tonkin-Hill G (2026). “Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy.” bioRxiv. doi:10.64898/2026.08.30.748153. https://www.biorxiv.org/content/10.64898/2026.08.30.748153v1.

Corresponding BibTeX entry:

  @Article{,
    title = {Accurate detection of metagenomic strain-level
      associations using average nucleotide identity with StrainSpy},
    author = {Sudaraka Mallawaarachchi and Kshitij Tandon and Nikhil
      Rajan and Vannessa Rossetto Marcelino and Shahneen Sandhu and
      Sammy Bedoui and Danielle J. Ingle and Ashray Gunjur and Gerry
      Tonkin-Hill},
    journal = {bioRxiv},
    year = {2026},
    doi = {10.64898/2026.08.30.748153},
    url =
      {https://www.biorxiv.org/content/10.64898/2026.08.30.748153v1},
  }