CapMux: a Snakemake pipeline for early demultiplexing of split-pool scRNA-seq data into sample-resolved outputs

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-resolved outputs.

CapMux supports workflows starting from either BCL files or FASTQ files and reconstructs sample identity by integrating sub-library index information with the experiment-specific barcoding plate layout. The pipeline was developed for the CapSeq method but is configurable for related scRNA-seq combinatorial barcoding designs through specification of barcode positions and experimental layout. CapMux resolves pooled data into outputs for each sample, enabling independent quality control summaries, mapping statistics, count matrices, and downstream visualizations.