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

Title:
DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments
Authors:
Trébeau, Céline, Boutet de Monvel, Jacques, Wong Jun Tai, Fabienne, Petit, Christine, Etournay, Raphael
Contributors:
Génétique et Physiologie de l'Audition, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut de la Vision, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Collège de France - Chaire Génétique et physiologie cellulaire, Collège de France (CdF (institution)), This work was supported by the European Research Council [ERC-2011-ADG_294570], LabEx LIFESENSES [ANR-10LABX-65], BNP Paribas Foundation, and LHW-Stiftung., ANR-11-IDEX-0004,SUPER,Sorbonne Universités à Paris pour l'Enseignement et la Recherche(2011), European Project: 294570,EC:FP7:ERC,ERC-2011-ADG_20110310,HAIRBUNDLE(2012)
Source:
Bioinformatics, 2019, ⟨10.1093/bioinformatics/bty1030⟩
Publisher Information:
CCSD; Oxford University Press (OUP), 2019.
Publication Year:
2019
Collection:
collection:INSERM
collection:PASTEUR
collection:CNRS
collection:CDF
collection:U968
collection:U1120
collection:PSL
collection:SORBONNE-UNIVERSITE
collection:SORBONNE-UNIV
collection:SU-MEDECINE
collection:SU-MED
collection:CDF-PSL
collection:SU-TI
collection:ANR
collection:ALLIANCE-SU
collection:INSTITUT-AUDITION
collection:SUPRA_-SVE6
Subject Terms:
[SDV.BIBS]Life Sciences [q-bio], Quantitative Methods [q-bio.QM], [SDV.BBM.BM]Life Sciences [q-bio], Biochemistry, Molecular Biology, Molecular biology, [SDV.BC.BC]Life Sciences [q-bio], Cellular Biology, Subcellular Processes [q-bio.SC]
Original Identifier:
PUBMED: 30576403
HAL:
Document Type:
Zeitschrift article<br />Journal articles
Language:
English
ISSN:
1367-4803
1367-4811
Relation:
info:eu-repo/semantics/altIdentifier/doi/10.1093/bioinformatics/bty1030; info:eu-repo/semantics/altIdentifier/pmid/30576403; info:eu-repo/grantAgreement/EC/FP7/294570/EU/Assembling the puzzle of the operating auditory hair bundle/HAIRBUNDLE
DOI:
10.1093/bioinformatics/bty1030
Access URL:
https://pasteur.hal.science/pasteur-02175109
https://pasteur.hal.science/pasteur-02175109v1/document
https://pasteur.hal.science/pasteur-02175109v1/file/Tre%CC%81beau%20et%20al.%20-%20DNABarcodeCompatibility%20an%20R-package%20for%20optimizi.pdf
Rights:
info:eu-repo/semantics/OpenAccess
URL: http://creativecommons.org/licenses/by/
Accession Number:
edshal.pasteur.02175109v1
Database:
HAL

Weitere Informationen

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