ddSeeker

ddSeeker processes Bio-Rad ddSEQ single-cell RNA-seq reads generated with Illumina sequencing to demultiplex reads and produce quality metrics for single-cell transcriptomic analysis.

Key Features:

• Tailored for ddSEQ Data: Addresses unique characteristics of Bio-Rad ddSEQ/Illumina sequencing reads that impede standard single-cell demultiplexing tools.
• Initial Processing and Quality Metrics: Performs initial processing and quality assessment of sequencing reads and outputs detailed quality metrics.
• Superior Performance: Recovers a higher rate of valid reads compared with Illumina BaseSpace, demonstrated on an Illumina test dataset and an in-house dataset with low and high sequencing quality.

Scientific Applications:

• Single-Cell Transcriptomics: Enables analysis of gene expression profiles at the individual cell level from Bio-Rad ddSEQ/Illumina scRNA-seq experiments.
• Quality Control in High-Throughput Sequencing: Provides metrics for assessing sequencing data quality to support downstream single-cell analyses.

Methodology:

Implements a specialized algorithm and specific demultiplexing strategies tailored to the unique structure of Bio-Rad ddSEQ/Illumina sequencing reads and performs initial processing steps including quality assessment and metric calculation.