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

Autor: Céline Trébeau, Christine Petit, Fabienne Wong Jun Tai, Jacques Boutet de Monvel, Raphaël Etournay
Přispěvatelé: Génétique et Physiologie de l'Audition, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut de la Vision, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), 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), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), 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, Etournay, Raphael, Sorbonne Universités à Paris pour l'Enseignement et la Recherche - - SUPER2011 - ANR-11-IDEX-0004 - IDEX - VALID, Assembling the puzzle of the operating auditory hair bundle - HAIRBUNDLE - - EC:FP7:ERC2012-12-01 - 2017-11-30 - 294570 - VALID
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Statistics and Probability
Source code
Library
Computer science
Interface (Java)
media_common.quotation_subject
[SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC]
Barcode
computer.software_genre
[SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry
Molecular Biology/Molecular biology
Biochemistry
DNA barcoding
law.invention
Set (abstract data type)
03 medical and health sciences
law
[SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC]
Multiplex
Nucleotide
Molecular Biology
030304 developmental biology
media_common
Gene Library
chemistry.chemical_classification
0303 health sciences
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Database
Base Sequence
030302 biochemistry & molecular biology
[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Molecular biology
DNA
Applications Notes
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Computer Science Applications
Computational Mathematics
Computational Theory and Mathematics
chemistry
Dna barcodes
Data and Text Mining
computer
Sequence Analysis
Software
Zdroj: Bioinformatics
Bioinformatics, Oxford University Press (OUP), 2019, ⟨10.1093/bioinformatics/bty1030⟩
Bioinformatics, 2019, ⟨10.1093/bioinformatics/bty1030⟩
ISSN: 1367-4803
1367-4811
Popis: 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 (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://github.com/comoto-pasteur-fr] under the GPL-2 licence. Supplementary information Supplementary data are available at Bioinformatics online.
Databáze: OpenAIRE
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