利用 SPLASH2 从原始测序读数中进行可扩展的无监督发现

IF 33.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Nature biotechnology Pub Date : 2024-09-23 DOI:10.1038/s41587-024-02381-2

Marek Kokot, Roozbeh Dehghannasiri, Tavor Baharav, Julia Salzman, Sebastian Deorowicz

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引用次数: 0

摘要

我们介绍了 SPLASH2，它是 SPLASH 的一种快速、可扩展的实现方法，基于一种高效的 k-mer 计数方法，用于检测来自各种测序技术和生物环境的海量数据集中的调节序列变异。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（Cancer Cell Line Encyclopedia）的大量 RNA-seq 数据中的生物学发现，包括癌症转录组中未标注的替代剪接和环状 RNA 的灵敏检测。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Scalable and unsupervised discovery from raw sequencing reads using SPLASH2

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.

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来源期刊

Nature biotechnology 工程技术-生物工程与应用微生物

CiteScore

63.00

自引率

1.70%

发文量

382

审稿时长

3 months

期刊介绍： Nature Biotechnology is a monthly journal that focuses on the science and business of biotechnology. It covers a wide range of topics including technology/methodology advancements in the biological, biomedical, agricultural, and environmental sciences. The journal also explores the commercial, political, ethical, legal, and societal aspects of this research. The journal serves researchers by providing peer-reviewed research papers in the field of biotechnology. It also serves the business community by delivering news about research developments. This approach ensures that both the scientific and business communities are well-informed and able to stay up-to-date on the latest advancements and opportunities in the field. Some key areas of interest in which the journal actively seeks research papers include molecular engineering of nucleic acids and proteins, molecular therapy, large-scale biology, computational biology, regenerative medicine, imaging technology, analytical biotechnology, applied immunology, food and agricultural biotechnology, and environmental biotechnology. In summary, Nature Biotechnology is a comprehensive journal that covers both the scientific and business aspects of biotechnology. It strives to provide researchers with valuable research papers and news while also delivering important scientific advancements to the business community.

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