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CountASAP:一个轻量级,易于使用的python包,用于处理ASAPseq数据

Christopher T Boughter¹, Budha Chatterjee², Yuko Ohta²

¹Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.

BMC bioinformatics

|November 28, 2025

概括

CountASAP是一个新的Python包,可以处理ASAPseq数据,将FASTQ文件转换为下游分析的计数矩阵. 该工具通过为ASAPseq实验提供专业处理来增强单细胞基因组学研究.

科学领域:

单细胞多组体的单细胞多组体.
基因组学和转录基因组学
计算生物学是一种计算生物学.

背景情况:

单细胞测序技术正在迅速发展,使得详细的基因组和转录组分析成为可能.
通过测序 (ATAC) 结合通过测序 (ASAPseq) 选择抗原分析,可同时测量染色体可访问性和细胞表面标记物.
现有的软件并没有专门解决将ASAPseq表面标记器FASTQ数据重新格式化为可用的计数矩阵的问题.

研究的目的:

开发一个专门的软件工具来处理ASAPseq数据.
创建一个Python包,将ASAPseq FASTQ文件转换为下游生物信息分析的计数矩阵.

主要方法:

开发了CountASAP,这是一个用于ASAPseq数据处理的Python包.
实现了对序读数与细胞标识符和寡头进行并行匹配.
使用CITEseq数据对现有工具进行CountASAP对比.
通过新的 ASAPseq 数据集验证了 CountASAP.

主要成果:

CountASAP成功地将ASAPseq FASTQ文件转换为计数矩阵.
性能和用户友好性与基于类似数据的现有工具可比.
从ASAPseq数据中生成生物学上有意义的结果,与染色质可访问性数据相关联.

结论:

CountASAP是第一个专门为ASAPseq数据处理设计的工具.
该软件是高效的,用户友好的,容易安装.
CountASAP为单细胞多omics数据提供可靠的处理.

关键词:

ASAPseq, 多omics, scRNAseq, 生物信息学, 疫苗

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