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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 "DNABarcodeCompatibility" in publications use:'
type: software
title: 'DNABarcodeCompatibility: A Tool for Optimizing Combinations of DNA Barcodes
  Used in Multiplexed Experiments on Next Generation Sequencing Platforms'
version: 1.21.0
doi: 10.1093/bioinformatics/bty1030
abstract: The package allows one to obtain optimised combinations of DNA barcodes
  to be used for multiplex sequencing. In each barcode combination, barcodes are pooled
  with respect to Illumina chemistry constraints. Combinations can be filtered to
  keep those that are robust against substitution and insertion/deletion errors thereby
  facilitating the demultiplexing step. In addition, the package provides an optimiser
  function to further favor the selection of barcode combinations with least heterogeneity
  in barcode usage.
authors:
- family-names: Trébeau
  given-names: Céline
  email: ctrebeau@pasteur.fr
  orcid: https://orcid.org/0000-0001-6795-5379
- family-names: Monvel
  given-names: Jacques
  name-particle: Boutet de
  email: jacques.boutet-de-monvel@pasteur.fr
  orcid: https://orcid.org/0000-0001-6182-3527
- family-names: Etournay
  given-names: Raphaël
  email: raphael.etournay@pasteur.fr
  orcid: https://orcid.org/0000-0002-2441-9274
preferred-citation:
  type: article
  title: 'DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations
    in multiplex sequencing experiments'
  authors:
  - family-names: Trébeau
    given-names: Céline
    email: ctrebeau@pasteur.fr
    orcid: https://orcid.org/0000-0001-6795-5379
  - family-names: Monvel
    given-names: Jacques
    name-particle: Boutet de
    email: jacques.boutet-de-monvel@pasteur.fr
    orcid: https://orcid.org/0000-0001-6182-3527
  - family-names: Wong Jun Tai
    given-names: Fabienne
  - family-names: Petit
    given-names: Christine
  - family-names: Etournay
    given-names: Raphaël
    email: raphael.etournay@pasteur.fr
    orcid: https://orcid.org/0000-0002-2441-9274
  issn: 1367-4811
  doi: 10.1093/bioinformatics/bty1030
  abstract: 'Summary: Using adequate DNA barcodes is essential to unambiguously identify
    each DNA library within a multiplexed set of libraries sequenced using next-generation
    sequencers. We introduce DNABarcodeCompatibility, an R-package that allows one
    to design single or dual-barcoding multiplex experiments by imposing desired constraints
    on the barcodes (including sequencer chemistry, barcode pairwise minimal distance,
    and nucleotide content), while optimizing barcode frequency usage, thereby allowing
    one to both facilitate the demultiplexing step and spare expensive library-preparation
    kits. The package comes with a user-friendly interface and a web app developed
    in Java and Shiny, respectively, with the aim to help bridge the expertise of
    core facilities with the experimental needs of non-experienced users. Availability
    and implementation: DNABarcodeCompatibility can be easily extended to fulfil specific
    project needs. The source codes of the R-package and its user interfaces are publicly
    available along with documentation at [https://github.com/comoto-pasteur-fr] under
    the GPL-2 licence. SUPPLEMENTARY INFORMATION: SUPPLEMENTARY DATA ARE AVAILABLE
    AT BIOINFORMATICS ONLINE.'
  journal: Bioinformatics (Oxford, England)
  month: '12'
  year: '2018'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/comoto-pasteur-fr/DNABarcodeCompatibility
url: https://github.com/comoto-pasteur-fr/DNABarcodeCompatibility
contact:
- family-names: Trébeau
  given-names: Céline
  email: ctrebeau@pasteur.fr
  orcid: https://orcid.org/0000-0001-6795-5379