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Updated: Sep 28, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

BarWare: efficient software tools for barcoded single-cell genomics.

Elliott Swanson^1,2, Julian Reading¹, Lucas T Graybuck³

¹Allen Institute for Immunology, Seattle, WA, USA.

BMC Bioinformatics

|March 29, 2022

Summary

This summary is machine-generated.

We developed BarWare, a computational pipeline for demultiplexing single-cell RNA sequencing data. This tool efficiently deconvolutes pooled samples, improving large-scale genomics studies.

Keywords:

Cell hashing Demultiplexing Genomics Single-cell RNA-seq

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Last Updated: Sep 28, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Barcode-based multiplexing enhances throughput and reduces batch effects in large single-cell genomics studies.
Challenges exist in deconvoluting multiplexed data to assign cells to their original samples.

Purpose of the Study:

To develop computational tools for efficient sample deconvolution in large-scale single-cell genomics.
To address the need for accurate cell origin assignment in multiplexed scRNA-seq data.

Main Methods:

Developed BarWare, a pipeline comprising BarCounter and BarMixer tools.
BarCounter quantifies barcode counts; BarMixer deconvolutes mixed single-cell data.
Utilized shell scripting for modular tool integration.

Main Results:

BarWare enables efficient demultiplexing of 10x Genomics scRNA-seq data from multiple wells.
The pipeline supports large sequencing projects with hashed samples.
Provides sample-specific files after deconvolution.

Conclusions:

BarWare offers a modular solution for barcode sequence quantification and data deconvolution.
Includes BarCounter (C implementation) and BarMixer (R package).
Freely available for non-commercial use, facilitating large-scale single-cell genomics research.