Barcode Identification for Single Cell Genomics

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2019 Jan 19

PMID 30654736

Citations 12

Authors

Akshay Tambe

Lior Pachter

Affiliations

Soon will be listed here.

Abstract

Background: Single-cell sequencing experiments use short DNA barcode 'tags' to identify reads that originate from the same cell. In order to recover single-cell information from such experiments, reads must be grouped based on their barcode tag, a crucial processing step that precedes other computations. However, this step can be difficult due to high rates of mismatch and deletion errors that can afflict barcodes.

Results: Here we present an approach to identify and error-correct barcodes by traversing the de Bruijn graph of circularized barcode k-mers. Our approach is based on the observation that circularizing a barcode sequence can yield error-free k-mers even when the size of k is large relative to the length of the barcode sequence, a regime which is typical single-cell barcoding applications. This allows for assignment of reads to consensus fingerprints constructed from k-mers.

Conclusion: We show that for single-cell RNA-Seq circularization improves the recovery of accurate single-cell transcriptome estimates, especially when there are a high number of errors per read. This approach is robust to the type of error (mismatch, insertion, deletion), as well as to the relative abundances of the cells. Sircel, a software package that implements this approach is described and publically available.

Citing Articles

A survey of k-mer methods and applications in bioinformatics.

Moeckel C, Mareboina M, Konnaris M, Chan C, Mouratidis I, Montgomery A Comput Struct Biotechnol J. 2024; 23:2289-2303.

PMID: 38840832 PMC: 11152613. DOI: 10.1016/j.csbj.2024.05.025.

Single cell RNA-seq: a novel tool to unravel virus-host interplay.

Jogi H, Smaraki N, Nayak S, Rajawat D, Kamothi D, Panigrahi M Virusdisease. 2024; 35(1):41-54.

PMID: 38817399 PMC: 11133279. DOI: 10.1007/s13337-024-00859-w.

Sequencing the origins of life.

Jia T, Nishikawa S, Fujishima K BBA Adv. 2023; 2:100049.

PMID: 37082609 PMC: 10074849. DOI: 10.1016/j.bbadva.2022.100049.

Single-Cell RNA Sequencing of Bone Marrow Mesenchymal Stem Cells from the Elderly People.

Zhu D, Gao J, Tang C, Xu Z, Sun T Int J Stem Cells. 2021; 15(2):173-182.

PMID: 34711696 PMC: 9148839. DOI: 10.15283/ijsc21042.

Single-Cell Transcriptome Profiling Simulation Reveals the Impact of Sequencing Parameters and Algorithms on Clustering.

Liu Y, Wu A, Peng X, Liu X, Liu G, Liu L Life (Basel). 2021; 11(7).

PMID: 34357088 PMC: 8304014. DOI: 10.3390/life11070716.

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