摘要
      恢复高质量的宏基因组组装基因组（HQ MAGs）对于探索微生物组成和微生物表型关联至关重要。然而，用于此目的的多种测序平台和计算工具可能会让研究人员感到困惑，因此需要进行广泛的评估。在这里，我们系统地评估了流行计算工具和测序平台（即策略）的总共40种组合，包括8个组装器、8个宏基因组装盒器和4种测序技术，包括短读、长读和宏HiC测序。根据测序数据的可用性，我们确定了用于单个任务（例如组装和装箱）和组合（例如生成更多HQ MAG）的最佳工具。我们发现混合组件和基于metaHiC的装箱的组合表现最好，其次是混合组件和长读组件。更重要的是，长读和metaHiC测序都将更多的移动元件和抗生素抗性基因与细菌宿主联系起来，并提高了公共人类肠道参考基因组的质量，其中32%（34/105）的HQ MAG质量比统一人类胃肠道基因组目录第2版或新版本中的质量更好。
Abstract
Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for exploring microbial compositions and microbe–phenotype associations. However, multiple sequencing platforms and computational tools for this purpose may confuse researchers and thus call for extensive evaluation. Here, we systematically evaluated a total of 40 combinations of popular computational tools and sequencing platforms (i.e. strategies), involving eight assemblers, eight metagenomic binners and four sequencing technologies, including short-, long-read and metaHiC sequencing. We identified the best tools for the individual tasks (e.g. the assembly and binning) and combinations (e.g. generating more HQ-MAGs) depending on the availability of the sequencing data. We found that the combination of the hybrid assemblies and metaHiC-based binning performed best, followed by the hybrid and long-read assemblies. More importantly, both long-read and metaHiC sequencings link more mobile elements and antibiotic resistance genes to bacterial hosts and improve the quality of public human gut reference genomes with 32% (34/105) HQ-MAGs that were either of better quality than those in the Unified Human Gastrointestinal Genome catalog version 2 or novel.

https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbad162/7145904?login=false