Extracting, filtering and simulating cellular barcodes using CellBarcode tools

Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode ex...

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Bibliographic Details
Published in:Nature Computational Science Vol. 4; no. 2; pp. 128 - 143
Main Authors: Sun, Wenjie, Perkins, Meghan, Huyghe, Mathilde, Faraldo, Marisa M., Fre, Silvia, Perié, Leïla, Lyne, Anne-Marie
Format: Journal Article
Language:English
Published: United States Nature Publishing Group 01.02.2024
Nature
Nature Publishing Group US
Subjects:
Bar codes
Datasets
Decision trees
Deoxyribonucleic acid
DNA
DNA - genetics
DNA Barcoding, Taxonomic - methods
Experiments
Filtration
Gene sequencing
Life Sciences
Polymerase Chain Reaction
Quality control
Reproducibility of Results
Resource
Sequence Analysis, DNA - methods
Simulation
ISSN:2662-8457, 2662-8457
Online Access:Get full text
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Summary:Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.
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ISSN:2662-8457
2662-8457
DOI:10.1038/s43588-024-00595-7