Metagenomic sequencing provides a culture-independent avenue to investigate the complex microbial communities by constructing metagenome-assembled genomes (MAGs). A MAG represents a microbial genome by a group of sequences from genome assembly with similar characteristics. It enables us to identify novel species and understand their potential functions in a dynamic ecosystem. Many computational tools have been developed to construct and annotate MAGs from metagenomic sequencing, however, there is a prominent gap to comprehensively introduce their background and practical performance. In this paper, we have thoroughly investigated the computational tools designed for both upstream and downstream analyses, including metagenome assembly, metagenome binning, gene prediction, functional annotation, taxonomic classification, and profiling. We have categorized the commonly used tools into unique groups based on their functional background and introduced the underlying core algorithms and associated information to demonstrate a comparative outlook. Furthermore, we have emphasized the computational requisition and offered guidance to the users to select the most efficient tools. Finally, we have indicated current limitations, potential solutions, and future perspectives for further improving the tools of MAG construction and annotation. We believe that our work provides a consolidated resource for the current stage of MAG studies and shed light on the future development of more effective MAG analysis tools on metagenomic sequencing.

宏基因组测序提供了一种独立于培养物的途径，通过构建宏基因组组装基因组 (MAG) 来研究复杂的微生物群落。MAG 通过一组具有相似特征的基因组组装序列来表示微生物基因组。它使我们能够识别新物种并了解它们在动态生态系统中的潜在功能。已经开发了许多计算工具来构建和注释宏基因组测序的 MAG，但是，在全面介绍其背景和实际性能方面还存在显着差距。在本文中，我们深入研究了为上游和下游分析设计的计算工具，包括宏基因组组装、宏基因组分箱、基因预测、功能注释、分类学分类和分析。我们根据常用工具的功能背景将其分为不同的组，并介绍底层核心算法和相关信息以展示比较前景。此外，我们强调了计算要求，并为用户选择最有效的工具提供指导。最后，我们指出了当前的局限性、潜在的解决方案以及进一步改进 MAG 构建和注释工具的未来前景。我们相信，我们的工作为现阶段的 MAG 研究提供了综合资源，并为未来开发更有效的宏基因组测序 MAG 分析工具指明了方向。