BarWare: efficient software tools for barcoded single-cell genomics

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 eac...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 23; no. 1; pp. 106 - 14
Main Authors: Swanson, Elliott, Reading, Julian, Graybuck, Lucas T., Skene, Peter J.
Format: Journal Article
Language:English
Published: London BioMed Central 27.03.2022
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
Algorithms
Analysis
Automation
Bar codes
Bioinformatics
Biomedical and Life Sciences
Cell hashing
Computational Biology/Bioinformatics
Computational efficiency
Computer Appl. in Life Sciences
Computer applications
Datasets
Deconvolution
Demultiplexing
DNA barcoding
Electronic Data Processing
Experiments
Genomics
Genomics - methods
Hashing (Computers)
Life Sciences
Methods
Microarrays
Multiplexing
Quality Control
RNA sequencing
Single-cell RNA-seq
Software
Software development tools
Software utilities
Tagging
United States
Demultiplexing
Cell hashing
Single-cell RNA-seq
Genomics
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary: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 .
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-022-04620-2