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BMC Genomics. 2018 Dec 24;19(1):960. doi: 10.1186/s12864-018-5249-x.

ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data.

Author information

1
Bioinformatics Unit, Hospital of Prato, Prato, Italy.
2
Sandro Pitigliani Translational Research Unit, Hospital of Prato, Prato, Italy.
3
Sandro Pitigliani Medical Oncology Department, Hospital of Prato, Prato, Italy.
4
NGS Core Facility, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy.
5
Bioinformatics Unit, Hospital of Prato, Prato, Italy. matteo.benelli@uslcentro.toscana.it.

Abstract

BACKGROUND:

New single-cell isolation technologies are facilitating studies on the transcriptomics of individual cells. Bio-Rad ddSEQ is a droplet-based microfluidic system that, when coupled with downstream Illumina library preparation and sequencing, enables the monitoring of thousands of genes per cell. Sequenced reads show unique features that do not permit the use of freely available tools to perform single cell demultiplexing.

RESULTS:

We present ddSeeker, a tool to perform initial processing and quality metrics of reads generated through Bio-Rad ddSEQ/Illumina experiments. Its application to the Illumina test dataset demonstrates that ddSeeker performs better than Illumina BaseSpace software, enabling a higher recovery of valid reads. We also show its utility in the analysis of an in-house dataset including two read sets characterized by low and high sequencing quality. ddSeeker and its source code are available at https://github.com/cgplab/ddSeeker .

CONCLUSIONS:

ddSeeker is a freely available tool to perform initial processing and quality metrics of reads generated through Bio-Rad ddSEQ/Illumina single cell transcriptomic experiments.

KEYWORDS:

Bioinformatics; Single-cell transcriptomics; scRNA-seq

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