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isolateR:一个R包,用于从桑格测序数据中生成微生物库

Brendan Daisley¹, Sarah J Vancuren¹, Dylan J L Brettingham¹

¹Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.

Bioinformatics (Oxford, England)

|July 11, 2024

概括

isolateR通过自动化桑格序列处理和分类学分类来简化微生物识别. 这使得能够有效地创建菌株库,用于编目微生物多样性和发现新物种.

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.

背景情况:

标记基因的桑格测序对于微生物 (细菌,古生物,真菌) 的识别至关重要.
手动处理和BLAST的局限性阻碍了微生物多样性研究的有效菌株库生成.

研究的目的:

开发一个标准化和可扩展的管道,用于自动处理桑格序列数据.
促进创建全面的菌株库,用于微生物目录和新物种发现.

主要方法:

桑格序列文件的自动批量处理.
使用全球对齐进行分类学分类,以遵循国际命名体系的类型菌株数据库.
创建具有可定制的脱复制和多运行数据集成的菌株库.
交互式HTML输出,用于简化数据探索.

主要成果:

isolateR成功自动化了桑格序列分析和分类学分类.
该工具能够有效地生成菌株库,这对于微生物多样性编目至关重要.
对人类肠道数据集的基准测试表明,isolateR在揭示菌株水平上的微生物多样性方面的熟练程度.

结论:

isolateR解决了微生物菌株库生成的关键挑战.
该工具促进了一种更有针对性,更细致的方法来探索宿主内的微生物多样性.
isolateR促进了新型微生物物种的发现,并加强了编目工作.

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