Obtaining data from single-cell transcriptomic sequencing allows for the investigation of cell-specific gene expression patterns, which could not be addressed a few years ago. With the advancement of droplet-based protocols the number of studied cells continues to increase rapidly. This establishes the need for software tools for efficient processing of the produced large-scale datasets. We address this need by presenting RainDrop for fast gene-cell count matrix computation from single-cell RNA-seq data produced by 10x Genomics Chromium technology. RainDrop can process single-cell transcriptomic datasets consisting of 784 million reads sequenced from around 8.000 cells in less than 40 minutes on a standard workstation. It significantly outperforms the established Cell Ranger pipeline and the recently introduced Alevin tool in terms of runtime by a maximal (average) speedup of 30.4 (22.6) and 3.5 (2.4), respectively, while keeping high agreements of the generated results. RainDrop is a software tool for highly efficient processing of large-scale droplet-based single-cell RNA-seq datasets on standard workstations written in C++. It is available at https://gitlab.rlp.net/stnieble/raindrop .

中文翻译：

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RainDrop：基于液滴的单细胞RNA序列读取的快速激活矩阵计算。

从单细胞转录组测序获得数据可以研究细胞特异性基因表达模式，这在几年前还没有解决。随着基于液滴的协议的发展，所研究的细胞数量继续迅速增加。这就需要有效处理所生成的大规模数据集的软件工具。我们通过展示RainDrop来满足这种需求，该技术可从10x Genomics Chromium技术产生的单细胞RNA-seq数据中快速计算基因细胞计数矩阵。RainDrop可以在不到40分钟的标准工作站上处理单细胞转录组数据集，该数据集由7.80亿个读物组成，这些读物在不到40分钟的时间内从约8.000个细胞中测序而来。在运行时方面，它的最大（平均）加速分别达到了30.4（22.6）和3.5（2.4），大大超过了已建立的Cell Ranger管道和最近推出的Alevin工具，同时保持了所生成结果的高度一致性。RainDrop是一种软件工具，用于在用C ++编写的标准工作站上高效处理大规模基于液滴的单细胞RNA-seq数据集。可从https://gitlab.rlp.net/stnieble/raindrop获得。