MVP:一个模块化的病毒学管道,用于识别,过,集群,注释和从元基因组中的垃圾桶病毒
Clément Coclet1, Antonio Pedro Camargo1, Simon Roux1
1DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
mSystems
|October 1, 2024
概括
模块化病毒学管道 (MVP) 简化了从复杂样本中进行病毒基因组分析. 这个用户友好的工具为研究人员标准化了病毒发现,注释和丰度计算.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 病毒学 病毒学
背景情况:
- 针对病毒学分析的专业管道的有限可用性.
- 对于具有有限生物信息学经验的研究人员来说,病毒基因组恢复,质量评估和注释的挑战.
- 病毒学工具的快速发展需要标准化的工作流程.
研究的目的:
- 介绍模块化病毒学管道 (MVP) v.1.0,一个用户友好的基于Python的管道用于标准的病毒学分析.
- 为病毒基因组识别,表征和丰度计算提供标准化和可复制的框架.
- 促进最先进的病毒学工具的整合,并确保该领域的持续相关性.
主要方法:
- 开发MVP,一个集成多个计算工具的模块化管道.
- 使用10个命令行执行模块,将MVP应用于来自湿地沉积物的20个元基因组.
- 利用诸如geNomad和CheckV等工具进行病毒基因组恢复,质量评估和注释.
主要成果:
- 从湿地沉积物转基因组中成功鉴定了11,656个病毒结合体和8,145个病毒操作分类单位 (vOTU).
- 在已识别的病毒群体中显示出明显的β-多样性模式.
- MVP为下游生态分析提供了全面的摘要.
结论:
- MVP提供了一个标准化,可复制和用户友好的解决方案,用于全面的病毒学分析.
- 管道的模块化设计允许轻松更新和整合新工具,确保长期的效用.
- MVP显著推进了对各种生态系统和样本类型的病毒生态学的研究.
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