从原始测序读取中进行可扩展且无监督的发现——SPLASH2
Scalable and unsupervised discovery from raw sequencing reads using SPLASH2
DOI 原文链接
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影响因子:41.7
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
DOI:
10.1038/s41587-024-02381-2
摘要
我们介绍了SPLASH2，一种基于高效k-mer计数方法的快速、可扩展的SPLASH实现，用于在来自各种测序技术和生物背景的海量数据集中检测受调控的序列变异。我们展示了SPLASH2在单细胞RNA测序（RNA-seq）数据和癌症细胞系百科全书（CCLE）中的生物学发现，包括癌症转录组中的未注释可变剪接和圆环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.