To cite anota2seq in publications use:

  Oertlin C. et al. (2019). Generally applicable transcriptome-wide
  analysis of translation using anota2seq Nucleic Acids Research URL
  https://academic.oup.com/nar/article/47/12/e70/5423604

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Generally applicable transcriptome-wide analysis of translation using anota2seq},
    author = {Christian Oertlin and Julie Lorent and Carl Murie and Luc Furic and Ivan Topisirovic and Ola Larsson},
    journal = {Nucleic Acids Research},
    year = {2019},
    url = {https://academic.oup.com/nar/article/47/12/e70/5423604},
    doi = {10.1093/nar/gkz223},
    publisher = {Oxford Academic},
  }