BarWare: efficient software tools for barcoded single-cell genomics

Abstract

Background Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. Despite advantages in flexibility of sample collection and scale, there are additional complications in the data deconvolution steps required to assign each cell to their originating samples. Results To meet computational needs for efficient sample deconvolution, we developed the tools BarCounter and BarMixer that compute barcode counts and deconvolute mixed single-cell data into sample-specific files, respectively. Together, these tools are implemented as the BarWare pipeline to support demultiplexing from large sequencing projects with many wells of hashed 10x Genomics scRNA-seq data. Conclusions BarWare is a modular set of tools linked by shell scripting: BarCounter, a computationally efficient barcode sequence quantification tool implemented in C; and BarMixer, an R package for identification of barcoded populations, merging barcoded data from multiple wells, and quality-control reporting related to scRNA-seq data. These tools and a self-contained implementation of the pipeline are freely available for non-commercial use at https://github.com/AllenInstitute/BarWare-pipeline.

Distinct Heterogeneity in the Naive T cell Compartments of Children and Adults

“…Libraries were sequenced on a Illuminia Novaseq platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare ( 39 ) to generate sample-specific output files. scRNA-seq Analysis.…”

“…( 13) TEA-seq Data Pre-processing. ADT and HTO count matrices were generated using BarCounter v1.0 (39). The RNA count matrix, and ADT count matrix were then combined into a single Seurat object.…”