模块化、高效且内存恒定的单细胞RNA测序预处理
Modular, efficient and constant-memory single-cell RNA-seq preprocessing.
作者信息
Melsted Páll, Booeshaghi A Sina, Liu Lauren, Gao Fan, Lu Lambda, Min Kyung Hoi Joseph, da Veiga Beltrame Eduardo, Hjörleifsson Kristján Eldjárn, Gehring Jase, Pachter Lior
机构信息
Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland.
Department of Mechanical Engineering, California Institute of Technology, Pasadena, CA, USA.
出版信息
Nat Biotechnol. 2021 Jul;39(7):813-818. doi: 10.1038/s41587-021-00870-2. Epub 2021 Apr 1.
We describe a workflow for preprocessing of single-cell RNA-sequencing data that balances efficiency and accuracy. Our workflow is based on the kallisto and bustools programs, and is near optimal in speed with a constant memory requirement providing scalability for arbitrarily large datasets. The workflow is modular, and we demonstrate its flexibility by showing how it can be used for RNA velocity analyses.
我们描述了一种用于单细胞RNA测序数据预处理的工作流程，该流程兼顾了效率和准确性。我们的工作流程基于kallisto和bustools程序，在速度上接近最优，具有恒定的内存需求，可为任意大的数据集提供可扩展性。该工作流程是模块化的，我们通过展示其如何用于RNA速度分析来证明其灵活性。
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