SoCloud: cloud-based data analysis for large-scale singlecell and single-nucleus RNA-seq

Massively parallel single cell RNA-Seq has opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so does the need for computational pipelines for scaled analysis. Here, we developed scCloud, a cloud-based framework for analyzing large scale single-cell and single-nucleus RNA-Seq datasets. scCloud combines the power of cloud computing with algorithm and implementation improvements to achieve high scalability, low cost, user-friendliness, and integrated support for a more comprehensive set of features. We benchmark scCloud on the Human Cell Atlas preview dataset of bone marrow cells and show that it substantially improves efficiency over conventional frameworks, while maintaining or improving the quality of results, enabling large-scale studies.