Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools

Cellular barcoding is a lineage-tracing methodology that couples heritable synthetic barcodes to high-throughput sequencing, enabling the accurate tracing of cell lineages across a range of biological contexts. Recent studies have extended these methods by incorporating lineage information into single-cell or spatial transcriptomics readouts. Leveraging the rich biological information within these datasets requires dedicated computational tools for dataset pre-processing and analysis. Here, we present BARtab, a portable and scalable Nextflow pipeline, and bartools, an open-source R package, designed to provide an integrated end-to-end cellular barcoding analysis toolkit. BARtab and bartools contain methods to simplify the extraction, quality control, analysis, and visualization of lineage barcodes from population-level, single-cell, and spatial transcriptomics experiments. We showcase the utility of our integrated BARtab and bartools workflow via the analysis of exemplar bulk, single-cell, and spatial transcriptomics experiments containing cellular barcoding information.