加快生物信息学在公共卫生中的应用
Kevin G Libuit1, Emma L Doughty1, James R Otieno1
1Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA.
Microbial genomics
|July 10, 2023
概括
使用Terra和Theiagen工作流的开放生物信息生态系统满足公共卫生实验室对标准化,可重复的基因组分析的需求. 这种可扩展的解决方案支持基因组流行病学,并已用于全球超过500万个样本分析.
科学领域:
- 生物信息学是一种生物信息学.
- 基因组流行病学 基因组流行病学
- 公共卫生 实验室 科学 公共卫生 实验室 科学
背景情况:
- 在公共卫生实验室 (PHLs) 中实施生物信息学面临着标准化,可重现性和可扩展性的挑战.
- PHL需要安全,可移植和可审计的数据分析解决方案,以适应运营约束.
- 现有的生物信息学工具可能无法满足公共卫生从业人员的特定需求.
研究的目的:
- 为公共卫生实验室建立一个开放的生物信息生态系统.
- 为基因组分析提供标准化,用户友好的生物信息学工作流程.
- 加强PHLs内的基因组流行病学能力.
主要方法:
- 利用Terra,一个基于Web的平台,具有图形用户界面,用于可访问的生物信息学分析.
- 开发了用于基因组组装,质量控制,表征和遗传学分析的Theiagen工作流程.
- 采用开源,容器化软件和WDL用于标准化和互操作性,代码可在Dockstore和GitHub上找到.
主要成果:
- 基因工作流产生标准化的输出,用于下游分析和可视化.
- 该生态系统已被40多个国家的90多个PHL采用.
- 在过去两年中,使用这些工作流进行了超过500万个样本分析.
结论:
- 开发的开放生物信息生态系统有效地满足了PHLs生物信息实施的要求.
- 泰拉平台和Theiagen工作流程为基因组流行病学提供了一个可扩展,可复制和可审计的解决方案.
- 持续开发和采用这种生态系统将进一步使全球公共卫生实验室受益.
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