Novel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics. This audience requires tools that are easy to use. Such need has been addressed by several genome annotation tools and pipelines. Visualizing resulting annotation is a crucial step of quality control. The UCSC Genome Browser is a powerful and popular genome visualization tool. Assembly Hubs, which can be hosted on any publicly available web server, allow browsing genomes via UCSC Genome Browser servers. The steps for creating custom Assembly Hubs are well documented and the required tools are publicly available. However, the number of steps for creating a novel Assembly Hub is large. In some cases, the format of input files needs to be adapted, which is a difficult task for scientists without programming background. Here, we describe MakeHub, a novel command line tool that generates Assembly Hubs for the UCSC Genome Browser in a fully automated fashion. The pipeline also allows extending previously created Hubs by additional tracks. MakeHub is freely available for downloading at https://github.com/Gaius-Augustus/MakeHub.
随着测序成本的降低，越来越多的个体及小型研究团体可以负担得起对感兴趣的非模式生物的基因组测序费用。同时可以供具有不同背景的科学家使用的，在新基因组中注释蛋白质编码基因的工具已经被开发出来，例如，AUGUSTUS、GeneMark ES/ET、GlimmerHMM、SNAP和GeMoMa，以及BRAKER、WebAUGUSTUS和MAKER。这种基因预测工具的输出文件是一种类似表格的文本文件，格式为基因转换格式（GTF）或通用特征格式3（GFF3）。在所有基因组注释项目中，对预测的基因结构进行可视化是质量控制的关键步骤。许多基因组浏览器可实现基因组的可视化功能，例如UCSC基因组浏览器、JBrowse和GBrowse2。其中，UCSC基因组浏览器是一个功能强大且被科研工作者广泛使用的基因组可视化工具。装配hubs是一种可以托管在任意公共可用网络服务器上，允许通过UCSC基因组浏览器服务器来浏览基因组。目前，对于创建自定义装配hubs的步骤方法已有公开的说明教程，并且所需的工具亦是公开可用的。但是，创建新的装配hubs的步骤却很多。在某些情况下，研究者需要调整输入文件的格式，而这对于没有编程背景的科学家来说是一项困难的任务。因此，我们开发了一种新的命令行工具MakeHub，用于在命令行上实现将BRAKER、MAKER、GlimmerHMM、SNAP和GeMoMa多个软件输出的单个物种基因组注释信息完全自动生成UCSC装配hubs。此方法还允许通过增加轨道进而扩充先前创建的hubs。MakeHub 可以从https://github.com/Gaius-Augustus/MakeHub 免费获得。





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