Cumulus

Cumulus provides scalable cloud-based analysis of large-scale single-cell (sc) and single-nucleus (sn) RNA-seq datasets to support systematic tissue atlas construction and large-cohort single-cell studies.

Key Features:

• Cloud-Based Framework: Operates on cloud infrastructure to distribute computation for large sc/snRNA-seq datasets.
• Scalability and Efficiency: Implements optimized algorithmic implementations to improve computational scalability and performance on large datasets such as the Human Cell Atlas Census of Immune Cells.
• Comprehensive Feature Set: Integrates a wide range of analysis functionalities required for sc/snRNA-seq workflows.
• Interactive Visualization: Supports interactive visualization of single-cell data for exploration and interpretation.
• WDL Workflows and Dockerfiles: Provides Workflow Description Language (WDL) workflows and Dockerfiles for reproducible deployment.
• Benchmarking: Performance has been benchmarked on datasets including the Human Cell Atlas Census of Immune Cells.

Scientific Applications:

• Tissue atlas construction: Enables large-scale analyses for systematic tissue atlases in health and disease.
• Human Cell Atlas studies: Applicable to projects such as the Human Cell Atlas for large-cohort single-cell profiling.
• Immune cell profiling from bone marrow: Capable of handling extensive immune cell datasets derived from bone marrow samples.

Methodology:

Cumulus uses cloud computing with optimized algorithm implementations, provides WDL workflows and Dockerfiles for reproducible execution, and has been benchmarked against datasets including the Human Cell Atlas Census of Immune Cells.