citHeader("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:")

desc <- packageDescription("Rbowtie")
vers <- paste("R package version", desc$Version)

citEntry(entry="article",
	 title="Ultrafast and memory-efficient alignment of short DNA sequences to the human genome",
	 author=personList(as.person("Ben Langmead"),
	                   as.person("Cole Trapnell"),
   			   as.person("Mihai Pop"),
			   as.person("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",
	 textVersion="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)."
)

citEntry(entry="article",
	 title="Detection of splice junctions from paired-end RNA-seq data by SpliceMap",
	 author=personList(as.person("Kin Fai Au"),
	                   as.person("Hui Jiang"),
			   as.person("Lan Lin"),
			   as.person("Yi Xing"),
			   as.person("Wing Hung Wong")),
	 journal="Nucleic Acids Research",
	 volume="38",
	 number="14",
	 pages="4570--4578",
	 year=2010,
	 note="PMID:20371516",
	 doi="10.1093/nar/gkq211",
	 textVersion="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)."
)

citEntry(entry="unpublished",
	 title="Rbowtie: An R wrapper for bowtie and SpliceMap short read aligners",
	 author=personList(as.person("Florian Hahne"),
	                   as.person("Anita Lerch"),
			   as.person("Michael B Stadler")),
	 #journal="",
	 #year=,
	 note=vers,
	 textVersion=" Hahne F, Lerch A, Stadler MB. Rbowtie: An R wrapper for bowtie and SpliceMap short read aligners. (unpublished)"
)

citFooter("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.")
