Moab Desert Crust - Sample 4E

Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).未培养细菌和古菌（Uncultivated Bacteria and Archaea）占地球物种的绝大多数，但通过鸟枪测序法（shotgun sequencing）直接从环境中获取其基因组，直至近年才成为可能。为实现获取地球微生物全套遗传组分的目标，亟需能够加速高质量基因组获取的技术。本研究介绍了一套分析流程与数据产物，依托美国能源部系统生物学知识库（U.S. Department of Energy Systems Biology Knowledgebase，KBase）平台（http://www.kbase.us/），从微生物组中提取高质量宏基因组组装基因组（metagenome-assembled genomes，MAGs）。在KBase中，该流程为端到端模式，支持用户从初始测序读段直接处理至宏基因组组装基因组，后续可借助KBase的其他功能开展分析，包括系统发育定位、功能注释、代谢建模、泛基因组功能分析、RNA测序（RNA-Seq）等。尽管此类功能的部分模块可从其他资源单独获取，但KBase作为免费开放的计算资源，兼具直观易用性、数据互操作性与工具整合性，使其成为从微生物组中获取宏基因组组装基因组的独特高效平台。本工作流不仅为基因组提取流程的各关键步骤提供了工具支持，同时还提供了一个可拓展框架，用户可通过KBase软件开发工具包（Software Development Kit，SDK）添加额外的宏基因组组装基因组获取与分析工具。