CapMux: a Snakemake pipeline for early demultiplexing of split-pool scRNA-seq data into sample-resolved outputs (opens in new tab)

Single-cell RNA sequencing methods based on split-pool combinatorial barcoding enable high-throughput profiling, yet sample identity is often encoded during early barcoding steps rather than through the library index. Consequently, reads from multiple biological samples remain pooled, complicating per-sample analysis and selective extraction of samples of interest. Here, I present CapMux, a Snakemake-based pipeline for processing split-pool scRNA-seq data from raw sequencing files to sample-r...