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对肠道病毒基因组的补充见解:使用多种组装器和内置器进行短读和长读元基因组的比较基准

Huarui Wang¹, Chuqing Sun¹, Yun Li¹

¹Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.

|December 21, 2024

概括

对比组装工具对于人类肠道病毒研究至关重要. 结合多个组装器和测序技术 (下一代测序和第三代测序),显著提高病毒基因组的恢复.

科学领域:

微生物学微生物学
生物信息学是一种生物信息学.
基因组学就是基因组学.

背景情况:

转基因组组装的病毒基因组对于人类肠道病毒组研究至关重要.
缺乏对病毒基因组组装工具的比较评估,特别是对于下一代测序 (NGS) 和第三代测序 (TGS) 数据.

研究的目的:

用NGS和TGS数据比较评估各种组装工具用于病毒基因组识别的有效性.
评估不同组装器和测序技术的互补性,以最大限度地提高病毒基因组的恢复.

主要方法:

在使用Illumina和PacBio平台测序的95个VLP丰富便样本上评估了NGS,TGS和混合组装器.
评估MEGAHIT,metaFlye和混合SPAdes作为NGS,TGS和混合数据集的最佳.
我们比较了四种组合方法:CONCOCT,MetaBAT2,AVAMB和vRhyme.

主要成果:

MEGAHIT,metaFlye和混合SPAdes分别显示了NGS,TGS和混合组装的最佳性能.
结合组装剂增加了4.8321.7倍的非冗余高质量的病毒基因组.
NGS和TGS数据产生了最少重叠的病毒基因组,突出显示了数据类型的影响.
比起CONCOCT,MetaBAT2,AVAMB和vRhyme提供了一个比CONCOCT更好的平衡,包括包容性和分类学一致性.

结论:

工具的局限性挑战了基因组驱动的病毒发现.
建议将多个汇编器和测序技术结合起来,以实现全面的病毒基因组恢复.
迫切需要专门的组装工具,以优化肠道病毒组研究.

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