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DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments

Abstract : 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 multi-plex 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 (https://dnabarcodecompatibility.pasteur.fr), 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://
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https://hal-pasteur.archives-ouvertes.fr/pasteur-02175109
Contributor : Raphael Etournay <>
Submitted on : Friday, July 5, 2019 - 2:58:46 PM
Last modification on : Sunday, October 25, 2020 - 7:06:23 AM

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Distributed under a Creative Commons Attribution 4.0 International License

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Céline Trébeau, Jacques Boutet de Monvel, Fabienne Wong Jun Tai, Christine Petit, Raphael Etournay. DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments. Bioinformatics, Oxford University Press (OUP), 2018, ⟨10.1093/bioinformatics/bty1030⟩. ⟨pasteur-02175109⟩

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