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Updated: Jun 26, 2026
10:34
Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
A Lightweight Workflow for Targeted Long-Read Transcriptomic Profiling Using Oxford Nanopore Sequencing
1Department of Medical Genetics, Medical University Varna, Marin Drinov Str. 55, 9000 Varna, Bulgaria.
Methods and Protocols
|June 25, 2026
Summary
We developed a lightweight pipeline for targeted long-read RNA sequencing analysis using Oxford Nanopore Technologies (ONT) data. This reproducible workflow enables efficient gene expression profiling, even with limited computational resources.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Long-read sequencing offers portability for small-scale studies.
- Existing RNA-seq frameworks are resource-intensive and designed for whole-transcriptome analysis.
Purpose of the Study:
- To present a lightweight, reproducible computational pipeline for targeted long-read transcriptomic profiling.
- To enable efficient analysis of Oxford Nanopore Technologies (ONT) cDNA sequencing data.
Main Methods:
- Development of a computational pipeline for targeted alignment of ONT cDNA sequencing data.
- Utilized minimap2 for alignment to a custom transcript reference panel.
- Implemented reads-per-million (RPM) for gene-level read counting and normalization.
Main Results:
- Successfully evaluated the pipeline on FFPE colorectal carcinoma samples (MSI-high).
- Enabled rapid quantification of mismatch repair gene expression and detection of immune markers (CD8A, PDCD1, HAVCR2).
- Demonstrated applicability across multiplexed barcode samples.
Conclusions:
- The pipeline offers a simple, reproducible, and computationally efficient framework for targeted transcriptomic analysis.
- Facilitates the adoption of ONT-based transcriptomic profiling in resource-constrained environments.
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