Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
Curr Protoc. 2021 Sep;1(9):e242. doi: 10.1002/cpz1.242.
Whole-genome sequencing of prokaryotes is now readily available and affordable on next-generation sequencing platforms. However, the process of de novo assembly can be complicated and tedious for those without a background in computational biology, bioinformatics, or UNIX. Licenses for commercial bioinformatics software may be costly and limited in flexibility. GALAXY is a powerful graphical open-source code-free bioinformatics platform that is freely available on multiple public and private servers. Here, we describe a bacterial de novo assembly workflow using GALAXY. It performs de novo genome assembly using short reads, long reads, or a hybrid method using both short and long reads. Genome annotation, prediction of antimicrobial resistance genes, and multi-locus sequence typing are subsequently performed to characterize the draft genome. Performing genome assembly and annotation on this pipeline allows documentation, parameterization, and sharing, facilitating replication, reuse, and reproducibility of both data and methods. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Quality check of NGS reads Basic Protocol 2: De novo assembly using Unicycler Basic Protocol 3: Assembly quality check using QUAST and Bandage Basic Protocol 4: Genome annotation using Prokka Basic Protocol 5: Prediction of antimicrobial resistance genes (ARGs) Basic Protocol 6: Multi-locus sequence typing (MLST).
现在，基于下一代测序平台，原核生物的全基因组测序变得简便且价格实惠。然而，对于那些没有计算生物学、生物信息学或 UNIX 背景的人来说，从头组装的过程可能会很复杂和繁琐。商业生物信息学软件的许可证可能价格昂贵且灵活性有限。GALAXY 是一个功能强大的图形化开源无代码生物信息学平台，可在多个公共和私人服务器上免费使用。在这里，我们描述了一个使用 GALAXY 的细菌从头组装工作流程。它使用短读长、长读长或两者混合的方法进行从头基因组组装。随后进行基因组注释、预测抗菌药物抗性基因和多位点序列分型，以表征草案基因组。在该管道上执行基因组组装和注释允许文档记录、参数化和共享，从而促进数据和方法的复制、重用和可重复性。© 2021 威利父子公司。基础方案 1：NGS 读段质量检查基础方案 2：使用 Unicycler 进行从头组装基础方案 3：使用 QUAST 和 Bandage 进行组装质量检查基础方案 4：使用 Prokka 进行基因组注释基础方案 5：抗菌药物抗性基因（ARGs）预测基础方案 6：多位点序列分型（MLST）。
