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阿莱文-fry-atac 能够使用虚拟颜色对单细胞ATAC-seq 数据进行快速和内存节省的映射,以实现精确的基因组伪对齐

Noor Pratap Singh¹, Jamshed Khan¹, Rob Patro¹

¹Department of Computer Science, University of Maryland, College Park, MD 20742, United States.

Bioinformatics (Oxford, England)

|July 15, 2025

概括

我们开发了alevin-fry-atac,这是一种用于单细胞ATAC序列分析的新工具. 它使用虚拟颜色来实现更快,更有效地对大型基因组进行记忆映射,并与现有的方法相匹配.

科学领域:

基因组学就是基因组学.
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:

伪对齐加速了转录组和元基因组分析,但与大型基因组作斗争.
在单细胞基因组学中,可扩展性和内存效率对于处理大型基因组引用至关重要.

研究的目的:

引入使用"虚拟颜色"的新型伪对齐方案,以高效地映射到大型基因组引用.
开发和评估alevin-fry-atac,一个用于单细胞ATAC-seq数据处理的新工具.
为现有的单细胞ATAC-seq分析管道提供快速,节省内存和准确的替代方案.

主要方法:

实施了修改后的伪对齐方案,将引用分成"虚拟颜色".
在Rust和C++17中开发了alevin-fry-atac,用于单细胞ATAC-seq数据处理.
与Chromap和Cell Ranger的ATAC相比,alevin-fry-atac的性能进行了比较.

主要成果:

阿莱文-fry-atac 展示了高可扩展性,处理数据速度比 Chromap 快 2.8 倍,内存少 33%.
生成的峰值和集群与已确定的方法 (Chromap,Cell Ranger ATAC) 显示出高度一致.
虚拟色彩增强伪对齐使得直接映射到基因组.

结论:

阿莱文-fry-atac为单细胞ATAC-seq分析提供了一个快速,内存高效和准确的解决方案.
该工具可以与现有的单细胞RNA-seq处理工具 (alevin-fry) 集成.
阿莱文-fry-atac为单细胞基因组学分析的开源生态系统做出了贡献.

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