下一个流的nf-core/metatdenovo管道用于可复制的metatranscriptomes的注释,以及更多
Danilo Di Leo1, Emelie Nilsson1, Arianna Krinos2
1Department of Biology and Environmental Science, Linnéuniversitetet, Kalmar, Kalmar, Sweden.
PeerJ
|December 10, 2025
概括
用nf-core/metatdenovo简化了metatranscriptomics分析,这是一个新的工作流程,用于新的组装,量化和注释. 该工具提高了微生物生态学研究的可复制性和可访问性.
科学领域:
- 微生物生态学 微生物生态学
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 大转录组学,社区RNA的研究,在微生物生态学中对于实地调查和实验至关重要.
- 然而,对具有有限经验的研究人员来说,注释原始序列数据带来了计算挑战.
- 标准化和可重复的分析对于科学研究的透明度,可比性和长期可重复性至关重要.
研究的目的:
- 为生物学家简化转录基因组处理.
- 促进微生物生态学中标准化和可重复的分析.
- 引入nf-core/metatdenovo,一个基于Nextflow的工作流程,用于新的metatranscriptome组装,量化和注释.
主要方法:
- 开发nf-core/metatdenovo,一个基于Nextflow的计算工作流.
- 使用容器技术 (Docker,Singularity) 来进行可重复的软件提供.
- 确保跨多种计算平台 (独立,HPC,云) 的兼容性.
- 通过命令行或Seqera平台的Web界面提供访问.
主要成果:
- nf-core/metatdenovo允许FAIR (可查找,可访问,可互操作,可重复使用) 的元转录组分析.
- 该管道标准化了新的组装,量化和注释过程.
- 促进高质量,记录和可重复的metatranscriptome工作流程.
结论:
- nf-core/metatdenovo显著降低了生物学家进行复杂的元转录组分析的障碍.
- 该工作流促进了FAIR数据原则,并提高了微生物生态学研究的可复制性.
- 该工具支持强大的和透明的社区RNA测序数据处理.
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