CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
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DOI：
10.1038/s41592-023-01940-w
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发表时间：
2023-07-27
期刊：
影响因子：
48
通讯作者：
Tyson, Gene W.
中科院分区：
文献类型：
--
作者：
Chklovski, Alex;Parks, Donovan H.;Tyson, Gene W.
CheckM2是一种基于机器学习的工具，用于预测分离株、单细胞和宏基因组组装基因组的基因组质量。测序技术和生物信息学工具的进步极大地提高了从宏基因组数据中恢复微生物基因组的速度。宏基因组组装基因组（MAG）的质量评估是下游分析之前的关键步骤。在这里，我们提出了CheckM2，这是一种使用机器学习预测MAG基因组质量的改进方法。使用合成和实验数据，我们证明了CheckM2在准确性和计算速度方面优于现有工具。此外，CheckM2的数据库可以快速更新新的高质量参考基因组，包括仅由单个基因组代表的分类群。我们还表明，CheckM2准确地预测新谱系的MAG的基因组质量，即使是那些基因组大小减小的（例如，Patescibacteria和DPANN超门）。CheckM2提供了跨细菌和古细菌谱系的准确基因组质量预测，在从MAG推断生物学结论时增加了信心。
This work presents CheckM2, which is a machine learning-based tool to predict genome quality of isolate, single-cell and metagenome-assembled genomes.Advances in sequencing technologies and bioinformatics tools have dramatically increased the recovery rate of microbial genomes from metagenomic data. Assessing the quality of metagenome-assembled genomes (MAGs) is a critical step before downstream analysis. Here, we present CheckM2, an improved method of predicting genome quality of MAGs using machine learning. Using synthetic and experimental data, we demonstrate that CheckM2 outperforms existing tools in both accuracy and computational speed. In addition, CheckM2's database can be rapidly updated with new high-quality reference genomes, including taxa represented only by a single genome. We also show that CheckM2 accurately predicts genome quality for MAGs from novel lineages, even for those with reduced genome size (for example, Patescibacteria and the DPANN superphylum). CheckM2 provides accurate genome quality predictions across bacterial and archaeal lineages, giving increased confidence when inferring biological conclusions from MAGs.