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Scnanoseq:用于牛津纳米孔单细胞RNA测序的nf核管道

Austyn Trull¹, Elizabeth A Worthey^1,2, Lara Ianov^1,3

¹Institutional Research Core Program-Biological Data Science Core, University of Alabama at Birmingham, Birmingham, AL United States.

Bioinformatics (Oxford, England)

|September 4, 2025

概括

一个新的生物信息管道,nf-core/scnanoseq,分析长时间读取的单细胞RNA测序数据. 它提供基因和转录量化,而不需要短读数据,增强单细胞转录组学分析.

科学领域:

基因组学
生物信息学
分子生物学

背景情况:

长读单细胞RNA测序 (scRNA-seq) 可实现全长转录和异形量化.
从历史上看,scRNA-seq需要短读数据来纠正测序错误并识别细胞条形码.
测序和计算方法的进步已经减少了这种依赖,但工作流的限制仍然存在.

研究的目的:

提供nf-core/scnanoseq,一个模块化和便携的二次分析管道,用于长读scRNA-seq数据.
从长期读取的单细胞和单核RNA数据中实现精确的基因和转录水平量化.
解决单细胞转录学中可访问和可重复的计算工作流程的需求.

主要方法:

在nf核心框架内实施基于Nextflow的管道.
纳入单细胞和单核数据分析的最佳实践.
包括用于条码检测/校正,读取对齐,UMI复制,量化和质量控制的模块.

主要成果:

nf-core/scnanoseq从长时间读取的scRNA-seq数据提供基因和转录水平的量化.
该管道是可移植的,可扩展的,并确保在不同的计算环境中可重现的结果.
它为分析的数据提供了全面的质量控制报告.

结论:

nf-core/scnanoseq通过直接分析长时间读取的scRNA-seq数据来克服以前的局限性.
该管道增强了长时间阅读技术的实用性,以在单细胞水平上进行详细的转录基因研究.
它的可用性和框架促进了该领域的广泛采用和标准化.

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