Unité de Génétique et Physiologie de l'Audition, Département Neuroscience, Institut Pasteur, Paris, France.
UMRS 1120, Institut National de la Santé et de la Recherche Médicale, Paris, France.
Bioinformatics. 2019 Aug 1;35(15):2690-2691. doi: 10.1093/bioinformatics/bty1030.
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.
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 data are available at Bioinformatics online.
使用足够的 DNA 条形码对于在使用下一代测序仪对多重文库进行测序时，能够明确地识别每个 DNA 文库是至关重要的。我们引入了 DNABarcodeCompatibility，这是一个 R 包，允许通过对条形码（包括测序仪化学、条形码对最小距离和核苷酸含量）施加所需的约束，设计单重或双重条形码多重实验，同时优化条形码的频率使用，从而既能促进解复用步骤，又能节省昂贵的文库制备试剂盒。该软件包附带一个用户友好的界面和一个用 Java 和 Shiny 开发的网络应用程序（https://dnabarcodecompatibility.pasteur.fr），旨在帮助将核心设施的专业知识与非经验用户的实验需求联系起来。
DNABarcodeCompatibility 可以很容易地扩展以满足特定项目的需求。R 包及其用户界面的源代码以及文档可在 [https://github.com/comoto-pasteur-fr] 上获得，遵循 GPL-2 许可证。
补充数据可在 Bioinformatics 在线获得。
