BARtab & bartools: an integrated Nextflow pipeline and R package for the analysis of synthetic cellular barcodes in the genome and transcriptome

Abstract

AbstractCellular barcoding using heritable synthetic barcodes coupled to high throughput sequencing is a powerful technique for the accurate tracing of clonal lineages in a wide variety of biological contexts. Recent studies have integrated cellular barcoding with a single-cell transcriptomics readout, extending the capabilities of these lineage tracing methods to the single-cell level. However there remains a lack of scalable and standardised open-source tools to pre-process and visualise both population-level and single-cell level cellular barcoding datasets. To address these limitations, we developedBARtab, a portable and scalable Nextflow pipeline that automates upstream barcode extraction, quality control, filtering and enumeration from high throughput sequencing data; andbartools, an open-source R package that streamlines the analysis and visualisation of population and single-cell level cellular barcoding datasets.BARtabcontains additional methods for the extraction and annotation of transcribed barcodes from single-cell RNA-seq and spatial transcriptomics experiments, thus extending this analytical toolbox to also support novel expressed cellular barcoding methodologies. We showcase the integratedBARtabandbartoolsworkflow through comparison with previously published toolsets and via the analysis of exemplar bulk, single-cell, and spatial transcriptomics cellular barcoding datasets.