从鸟枪法宏基因组测序数据中恢复宏基因组组装基因组：方法、应用、挑战与机遇
Recovering metagenome-assembled genomes from shotgun metagenomic sequencing data: Methods, applications, challenges, and opportunities.
作者信息
Zhou Yunyan, Liu Min, Yang Jiawen
机构信息
State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China.
出版信息
Microbiol Res. 2022 Jul;260:127023. doi: 10.1016/j.micres.2022.127023. Epub 2022 Apr 8.
Reference genomes are essential for analyzing the metabolic and functional potentials of microbiomes. However, microbial genome resources are limited because most of microorganisms are difficult to culture. Genome binning is a culture-independent approach that can recover a vast number of microbial genomes from short-read high throughput shotgun metagenomic sequencing data. In this review, we summarize methods commonly used for reconstructing metagenome-assembled genomes (MAGs) to provide a reference for researchers to choose propriate software programs among the numerous and complicated tools and pipelines that are available for these analyses. In addition, we discuss application prospects, challenges, and opportunities for recovering MAGs from metagenomic sequencing data.
参考基因组对于分析微生物群落的代谢和功能潜力至关重要。然而，由于大多数微生物难以培养，微生物基因组资源有限。基因组分箱是一种不依赖培养的方法，它可以从短读长高通量鸟枪法宏基因组测序数据中获得大量微生物基因组。在本综述中，我们总结了常用于重建宏基因组组装基因组（MAG）的方法，以便在众多复杂的工具和流程中为研究人员选择合适的软件程序提供参考，这些工具和流程可用于这些分析。此外，我们还讨论了从宏基因组测序数据中获取MAG的应用前景、挑战和机遇。
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