BarWare

BarWare demultiplexes barcode-based single-cell sequencing data to assign cells to originating samples and produce merged, quality-controlled datasets for downstream 10x Genomics scRNA-seq analysis.

Key Features:

• Barcode-based multiplexing: Implements barcode-based multiplexing to enhance throughput and reduce batch effects in single-cell genomics experiments.
• Modular pipeline architecture: Comprises two primary components, BarCounter and BarMixer, integrated via shell scripting to form a cohesive demultiplexing workflow.
• BarCounter (C): Implemented in C to quantify barcode sequences by processing raw sequencing data and counting barcodes associated with individual cells.
• BarMixer (R): Implemented as an R package to identify barcoded cell populations, merge data from multiple wells, and generate quality-control reports specific to scRNA-seq.
• 10x Genomics scRNA-seq support: Tailored for hashed 10x Genomics scRNA-seq data and demultiplexing projects involving numerous wells.

Scientific Applications:

• Sample deconvolution: Assigns individual cells to their originating samples in multiplexed single-cell experiments.
• Large-scale scRNA-seq studies: Supports demultiplexing and merging of data from projects with many wells to enable high-throughput analyses.
• Batch-effect mitigation: Reduces batch effects introduced by separate sample processing through barcode-based multiplexing.
• Downstream single-cell analyses: Produces merged, quality-controlled datasets suitable for downstream transcriptomic analyses.
• Biological research domains: Applicable to studies in developmental biology, cancer research, and immunology that require single-cell resolution.

Methodology:

The pipeline uses BarCounter (C) to quantify barcodes from raw sequencing data, BarMixer (R) to identify barcoded cell populations, merge wells, and produce scRNA-seq quality-control reports, and integrates these components via shell scripting to perform demultiplexing of hashed 10x Genomics scRNA-seq data.