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).

  Gaidatzis D, Lerch A, Hahne F, Stadler MB. QuasR: Quantification and
  annotation of short reads in R. Bioinformatics 31(7):1130-1132
  (2015).

A BibTeX entry for LaTeX users is

  @Article{,
    title = {QuasR: Quantification and annotation of short reads in R},
    author = {Dimos Gaidatzis and Anita Lerch and Florian Hahne and Michael B Stadler},
    journal = {Bioinformatics},
    volume = {31},
    number = {7},
    pages = {1130--1132},
    year = {2015},
    note = {PMID:25417205},
    doi = {10.1093/bioinformatics/btu781},
  }

  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},
  }

  Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with
  low memory requirements. Nat Methods, 12(4):357-60 (2015).

A BibTeX entry for LaTeX users is

  @Article{,
    title = {HISAT: a fast spliced aligner with low memory requirements},
    author = {Daehwan Kim and Ben Langmead and Steven L Salzberg},
    journal = {Nature Methods},
    volume = {12},
    pages = {357--360},
    year = {2015},
    note = {PMID:25751142},
    doi = {10.1038/nmeth.3317},
  }

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.