The Rbowtie package contains code from two separate software projects.
If using bowtie only, it can be cited as Langmead et al. (2009). If
using also SpliceMap, it can be cited in addition Au et al. (2010). The
Rbowtie package can be cited using the third reference below:

  Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and
  memory-efficient alignment of short DNA sequences to the human
  genome. Genome Biology 10(3):R25 (2009).

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Ultrafast and memory-efficient alignment of short DNA sequences to the human genome},
    author = {Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg},
    journal = {Genome Biology},
    volume = {10},
    number = {3},
    pages = {R25},
    year = {2009},
    note = {PMID:19261174},
    doi = {10.1186/gb-2009-10-3-r25},
  }

  Au KF, Jiang H, Lin L, Xing Y, Wong WH. Detection of splice junctions
  from paired-end RNA-seq data by SpliceMap. Nucleic Acids Research,
  38(14):4570-8 (2010).

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Detection of splice junctions from paired-end RNA-seq data by SpliceMap},
    author = {Kin Fai Au and Hui Jiang and Lan Lin and Yi Xing and Wing Hung Wong},
    journal = {Nucleic Acids Research},
    volume = {38},
    number = {14},
    pages = {4570--4578},
    year = {2010},
    note = {PMID:20371516},
    doi = {10.1093/nar/gkq211},
  }

  Hahne F, Lerch A, Stadler MB. Rbowtie: An R wrapper for bowtie and
  SpliceMap short read aligners. (unpublished)

A BibTeX entry for LaTeX users is

  @Unpublished{,
    title = {Rbowtie: An R wrapper for bowtie and SpliceMap short read aligners},
    author = {Florian Hahne and Anita Lerch and Michael B Stadler},
    note = {R package version 1.45.0},
  }

This free open-source software implements academic research by the
authors and co-workers. If you use it, please support the project by
citing the appropriate journal articles.