rhapsodist: a reproducible Snakemake workflow for BD~Rhapsody single-cell RNA-seq data (opens in new tab)

BD Rhapsody is a widely used single-cell RNA-seq (scRNA-seq) platform to profile gene expression. Based on barcoded beads, processing BD Rhapsody experiments is demanding because of the multiple barcode versions and layouts, which makes it difficult to locate barcodes by scanning reads positionally. We introduce rhapsodist, a reproducible and scalable Snakemake workflow to process BD Rhapsody whole transcriptome analysis (WTA) data from raw FASTQ reads. As a result, rhapsodist generates count...