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).

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).

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

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 = {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},
  }

  @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},
  }

  @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},
  }