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).

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).

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 (unpublished)

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.

Corresponding BibTeX entries:

  @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},
  }

  @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},
  }

  @Unpublished{,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 1.53.0},
  }