To cite vivaldi in publications use:

AE R, KEE J, M K, M K, B W, S S, S B, A K, C M, J-H Y, R M, W W, D R, MI S, MJ M, M L, M Ł, S D, D G, E G (2022). “Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data.” bioRxiv. https://www.biorxiv.org/content/10.1101/2021.05.05.442873v2.

Corresponding BibTeX entry:

  @Article{,
    title = {Optimized Quantification of Intrahost Viral Diversity in
      SARS-CoV-2 and Influenza Virus Sequence Data},
    author = {Roder AE and Johnson KEE and Knoll M and Khalfan M and
      Wang B and Schultz-Cherry S and Banakis S and Kreitman A and
      Mederos C and Youn J-H and Mercado R and Wang W and Ruchnewitz D
      and Samanovic MI and Mulligan MJ and Lassig M and Łuksza M and
      Das S and Gresham D and Ghedin E},
    journal = {bioRxiv},
    year = {2022},
    url =
      {https://www.biorxiv.org/content/10.1101/2021.05.05.442873v2},
  }