Please cite Wei, Zheng, et al. "esATAC: an easy-to-use systematic
pipeline for ATAC-seq data analysis." Bioinformatics (2018) for using
Rbowtie2.

  Wei, Zheng, et al. "esATAC: an easy-to-use systematic pipeline for
  ATAC-seq data analysis." Bioinformatics (2018)

A BibTeX entry for LaTeX users is

  @Article{,
    title = {esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis},
    author = {Zheng Wei and Wei Zhang and Huan Fang and Yanda Li and Xiaowo Wang},
    journal = {Bioinformatics},
    year = {2018},
    pmid = {29522192},
    doi = {10.1093/bioinformatics/bty141},
  }