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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "Rbowtie" in publications use:'
type: software
license: Artistic-2.0
title: 'Rbowtie: R bowtie wrapper'
version: 1.45.0
doi: 10.1186/gb-2009-10-3-r25
abstract: This package provides an R wrapper around the popular bowtie short read
  aligner and around SpliceMap, a de novo splice junction discovery and alignment
  tool. The package is used by the QuasR bioconductor package. We recommend to use
  the QuasR package instead of using Rbowtie directly.
authors:
- family-names: Hahne
  given-names: Florian
- family-names: Lerch
  given-names: Anita
- family-names: Stadler
  given-names: Michael
  email: michael.stadler@fmi.ch
  orcid: https://orcid.org/0000-0002-2269-4934
preferred-citation:
  type: article
  title: Ultrafast and memory-efficient alignment of short DNA sequences to the human
    genome
  authors:
  - family-names: Langmead
    given-names: Ben
  - family-names: Trapnell
    given-names: Cole
  - family-names: Pop
    given-names: Mihai
  - family-names: Salzberg
    given-names: Steven L
  journal: Genome Biology
  volume: '10'
  issue: '3'
  year: '2009'
  notes: PMID:19261174
  doi: 10.1186/gb-2009-10-3-r25
  start: R25
repository: https://bioc.r-universe.dev
repository-code: https://github.com/fmicompbio/Rbowtie
url: https://github.com/fmicompbio/Rbowtie
date-released: '2023-01-29'
contact:
- family-names: Stadler
  given-names: Michael
  email: michael.stadler@fmi.ch
  orcid: https://orcid.org/0000-0002-2269-4934
references:
- type: article
  title: Detection of splice junctions from paired-end RNA-seq data by SpliceMap
  authors:
  - family-names: Au
    given-names: Kin Fai
  - family-names: Jiang
    given-names: Hui
  - family-names: Lin
    given-names: Lan
  - family-names: Xing
    given-names: Yi
  - family-names: Wong
    given-names: Wing Hung
  journal: Nucleic Acids Research
  volume: '38'
  issue: '14'
  year: '2010'
  notes: PMID:20371516
  doi: 10.1093/nar/gkq211
  start: '4570'
  end: '4578'
- type: unpublished
  title: 'Rbowtie: An R wrapper for bowtie and SpliceMap short read aligners'
  authors:
  - family-names: Hahne
    given-names: Florian
  - family-names: Lerch
    given-names: Anita
  - family-names: Stadler
    given-names: Michael B
  notes: R package version 1.45.0