BacPipe：一种用于临床诊断细菌学的快速、用户友好的全基因组测序流程。
BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology.
作者信息
Xavier Basil B, Mysara Mohamed, Bolzan Mattia, Ribeiro-Gonçalves Bruno, Alako Blaise T F, Harrison Peter, Lammens Christine, Kumar-Singh Samir, Goossens Herman, Carriço João A, Cochrane Guy, Malhotra-Kumar Surbhi
机构信息
Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium.
Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium; Microbiology Unit, Belgian Nuclear Research Center (SCK•CEN), Mol 2400, Belgium.
出版信息
iScience. 2020 Jan 24;23(1):100769. doi: 10.1016/j.isci.2019.100769. Epub 2019 Dec 12.
Despite rapid advances in whole genome sequencing (WGS) technologies, their integration into routine microbiological diagnostics has been hampered by the lack of standardized downstream bioinformatics analysis. We developed a comprehensive and computationally low-resource bioinformatics pipeline (BacPipe) enabling direct analyses of bacterial whole-genome sequences (raw reads or contigs) obtained from second- or third-generation sequencing technologies. A graphical user interface was developed to visualize real-time progression of the analysis. The scalability and speed of BacPipe in handling large datasets was demonstrated using 4,139 Illumina paired-end sequence files of publicly available bacterial genomes (2.9-5.4 Mb) from the European Nucleotide Archive. BacPipe is integrated in EBI-SELECTA, a project-specific portal (H2020-COMPARE), and is available as an independent docker image that can be used across Windows- and Unix-based systems. BacPipe offers a fully automated "one-stop" bacterial WGS analysis pipeline to overcome the major hurdle of WGS data analysis in hospitals and public-health and for infection control monitoring.
尽管全基因组测序（WGS）技术取得了快速进展，但由于缺乏标准化的下游生物信息学分析，这些技术在常规微生物诊断中的整合受到了阻碍。我们开发了一种全面且计算资源需求低的生物信息学流程（BacPipe），能够直接分析从第二代或第三代测序技术获得的细菌全基因组序列（原始 reads 或 contigs）。我们开发了一个图形用户界面来可视化分析的实时进展。使用来自欧洲核苷酸档案馆的 4139 个公开可用细菌基因组（2.9 - 5.4 Mb）的 Illumina 双端序列文件，展示了 BacPipe 在处理大型数据集时的可扩展性和速度。BacPipe 集成在 EBI - SELECTA（一个特定项目门户，H2020 - COMPARE）中，并作为一个独立的 Docker 镜像提供，可在基于 Windows 和 Unix 的系统中使用。BacPipe 提供了一个全自动的“一站式”细菌 WGS 分析流程，以克服医院、公共卫生和感染控制监测中 WGS 数据分析的主要障碍。
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