对于特征化大肠杆菌和沙门氏菌基因组的GEA管道
Aaron M Dickey1, John W Schmidt2, James L Bono2
1US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, 844 Rd 313, PO Box 165, Clay Center, NE, 68933, USA. aaron.dickey@usda.gov.
Scientific reports
|June 10, 2024
概括
通过使用最新的数据库,GEA管道有效地注释了大量的Salmonella enterica和Escherichia coli基因组. 这种工具有助于对这些主要的食源性病原体进行临床监测.
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:
- 沙门氏菌 (Salmonella enterica) 和大肠杆菌 (Escherichia coli) 是重要的食物传播病原体,需要基因组监测.
- 现有的计算管道需要整合更新的注释数据库,以便准确的病原体分析.
研究的目的:
- 开发和介绍基因组注释 (GEA) 管道,用于大肠杆菌和S. enterica基因组的大规模分析.
- 通过整合基因组流行病学中心 (CGE) 工具来增强基因组注释.
主要方法:
- 该GEA管道接受原始的Illumina读取或预先组装的E. coli和S. enterica.的基因组.
- 它执行基因组组合和注释,或提供组合的直接注释.
- 使用CGE命令行工具和高性能计算以提高效率.
主要成果:
- 该管道提供了tab-delimited格式的预测基因组注释.
- 通过超过14000个沙门氏菌基因组组合,证明了大规模注释能力.
- 在不同的计算环境中确认了大肠杆菌原始读数的可复制性.
结论:
- GEA的管道被优化为高性能计算,使高效,大规模的基因组表征.
- 它支持对E. coli和S. enterica.等关键的食源性病原体进行最新的基因组监测.
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