citHeader("Please use the QuasR reference below to cite the software itself.
If you were using qAlign with Rbowtie as aligner, it can be cited as Langmead et al. (2009) (unspliced alignments)
or Au et al. (2010) (spliced alignments).
If you were using qAlign with Rhisat2 as aligner, it can be cited as Kim et al. (2015).")

citEntry(entry="article",
	 title="QuasR: Quantification and annotation of short reads in R",
	 author=personList(as.person("Dimos Gaidatzis"),
			   as.person("Anita Lerch"),
                           as.person("Florian Hahne"),
			   as.person("Michael B Stadler")),
	 journal="Bioinformatics",
         volume="31",
         number="7",
         pages="1130--1132",
	 year=2015,
	 note="PMID:25417205",
         doi="10.1093/bioinformatics/btu781",
	 textVersion="Gaidatzis D, Lerch A, Hahne F, Stadler MB. QuasR: Quantification and annotation of short reads in R. Bioinformatics 31(7):1130-1132 (2015)."
)

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="article",
  title="HISAT: a fast spliced aligner with low memory requirements",
  author=personList(as.person("Daehwan Kim"),
                    as.person("Ben Langmead"),
                    as.person("Steven L Salzberg")),
  journal="Nature Methods",
  volume="12",
  pages="357--360",
  year=2015,
  note="PMID:25751142",
  doi="10.1038/nmeth.3317",
  textVersion="Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods, 12(4):357-60 (2015)."
)

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.")
