SPLASH2：基于原始测序读取的可扩展无监督发现方法
Scalable and unsupervised discovery from raw sequencing reads using SPLASH2
影响因子:41.70000
分区:生物学1区 Top / 生物工程与应用微生物1区
发表日期:2025 Jul
作者:
Marek Kokot, Roozbeh Dehghannasiri, Tavor Baharav, Julia Salzman, Sebastian Deorowicz
摘要
我们提出了SPLASH2，一种基于高效k-mer计数方法的快速、可扩展的实现，用于在大规模测序数据和多种生物学背景中检测调控序列变异。通过在单细胞RNA测序（RNA-seq）和癌症细胞系百科全书（CCLE）中的应用，展示了SPLASH2在生物学发现方面的潜力，包括癌症转录组中的未注释可变剪接以及圆环RNA的敏感检测。
Abstract
We introduce SPLASH2, a fast, scalable implementation of SPLASH based on an efficient k-mer counting approach for regulated sequence variation detection in massive datasets from a wide range of sequencing technologies and biological contexts. We demonstrate biological discovery by SPLASH2 in single-cell RNA sequencing (RNA-seq) data and in bulk RNA-seq data from the Cancer Cell Line Encyclopedia, including unannotated alternative splicing in cancer transcriptomes and sensitive detection of circular RNA.