SMART-Seq mRNA Long Read Demultiplexing for ONT Sequencing Data
Overview
SMART-Seq mRNA Long Read (LR) provides the excellent sensitivity needed to obtain full-length transcript information from high-integrity total RNA (RIN ≥8) or intact cells, enabling reliable analysis of transcript isoforms, gene fusions, and more. After obtaining your FASTQ output from Oxford Nanonpore (ONT) sequencers—what should you do next?
Use Dorado, ONT's open source basecaller, along with configuration files tailored for SMART-Seq LR sequencing output to demultiplex the raw data for restranding, genome alignment, and beyond.
Follow the directions in the SMART-Seq mRNA Long Read Demultiplexing Protocol-At-A-Glance for ONT Sequencing Data to prepare your system and perform the bioinformatics transformation to gain scientific insights into your experimental samples.
Supported operating systems & hardware guidelines
- These instructions have been tested on Linux RedHat 9.5
- For more information about hardware requirements, refer to the official Dorado documentation
Third-party software dependencies*
- dorado 0.8.3+98456f7, 0.9.0+9dc15a8, 0.9.1+c8c2c9f, or higher (Github link)
- Optional, but recommended: Restrander (Github link)
*Not included with the downloads; must be downloaded and installed separately.
Additional product information
More information is available in the SMART-Seq mRNA Long Read Demultiplexing Protocol-At-A-Glance for ONT Sequencing Data.
SMART-Seq mRNA Long Read Demultiplexing procedure version history
| Version number | Release date |
Notes |
|---|---|---|
| v1.0 | 2025-03-14 |
|
Buy now: SMART-Seq mRNA Long Read
Generate high-quality, long-read, barcoded cDNA from 1–1,000 intact cells or 10 pg–100 ng of total RNA.
Learn more: Enabling long-read RNA sequencing from low-input samples
Facilitating the discovery of complex isoforms and novel structural variants from 10 pg–100 ng of total RNA
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