WASP

WASP processes and analyzes Drop-Seq-based single-cell RNA-seq (scRNA-seq) data from protocols such as ddSEQ and 10x Genomics to perform quality control, demultiplexing, reference alignment, and generation of gene expression matrices for downstream analyses.

Key Features:

• Supported sequencing protocols: Supports Drop-Seq-based scRNA-seq datasets generated using ddSEQ and 10x Genomics protocols.
• Raw read processing and quality control: Processes raw reads and produces initial quality control metrics.
• Demultiplexing and reference alignment: Performs demultiplexing and aligns reads to a reference to enable assignment of reads to cells.
• Gene expression matrix generation and metrics: Generates demultiplexed gene expression matrices accompanied by quality metrics.
• Modular input handling: Accepts pre-processed gene expression matrices from external sources as well as matrices produced by its own processing steps.
• Downstream analyses: Supports detection of differentially expressed genes, clustering of cellular populations, and graphical visualization of results.

Scientific Applications:

• Cellular heterogeneity analysis: Enables identification and characterization of (sub-)cellular populations and cell-type specific expression patterns.
• Domain-specific research: Applicable to developmental biology, oncology, immunology, and regenerative medicine for cell-resolved gene expression studies.

Methodology:

Initial quality control, demultiplexing, reference alignment, generation of demultiplexed gene expression matrices and quality metrics, handling of pre-processed matrices, detection of differentially expressed genes, clustering of cellular populations, and graphical visualization.