Selecting the sequencing technique and approach that best fits your requirements can be challenging, especially given the number of variables to consider. One of these factors is resolution, specifically genomic resolution or read resolution. While genomic resolution refers to a sequencing technology’s ability to identify variations in the genome (e.g., base-pair resolution with WGS or structural variants with array-based methods), the focus here is on the latter. The read resolution relates to the length and quality of the sequencing reads, making a general distinction between two techniques: Short-read and Long-read technologies.
The read resolution refers to the amount of information an individual DNA or RNA fragment contains and how well this can be mapped using a reference genome or assembled de novo. Short-read sequencing (e.g. Illumina) typically achieves 50 – 300 base pairs while long reads can reach lengths of thousands to millions of base pairs per read. One is not always better than the other; the approach is different, but the choice depends on the considered variables.
The workhorse or the innovation
While short-read sequencing has been the workhorse of genomics for years, it often struggles with repetitive regions, structural variants, and the detection of full-length transcripts. That’s where long-read sequencing steps in, capturing entire genes, complex variants, and repetitive regions in a single read. The result?
- More accurate genome assemblies
- Better detection of isoforms and splice variants
- Improved analysis of structural variants and epigenetic modifications
- Superior insights into complex organisms like fungi, plants, and cancer genomes
- Enhanced resolution for clinical research, including rare disease detection and cancer genomics
PacBio or ONT?
Both platforms have transformed genomics through long-read sequencing, but each has unique strengths depending on your research goals.
PacBio (HiFi reads)
- Extremely high accuracy (>99.9%)
- Ideal for de novo assemblies, structural variant detection, and clinical-grade applications
- Long, highly accurate reads (HiFi)
When to use PaBio?
- Choose PacBio when you need the highest accuracy for complex assemblies or sensitive clinical applications.
Oxford Nanopore Technologies
- Ultra-long reads (up to millions of bases)
- Real-time sequencing and analysis
- Direct detection of epigenetic modifications and native RNA
When to use ONT?
- Opt for ONT when flexibility, ultra-long reads, or real-time data is key (especially in fieldwork or rapid response scenarios).
Both technologies are powerful. In some cases, a hybrid sequencing strategy that combines different approaches (i.e. long read and short read sequencing) may be your perfect solution to answer complex questions.
Sequencing with ONT
Unlike traditional methods, Oxford Nanopore enables real-time sequencing of single DNA or RNA molecules, without the need for amplification. Here’s how it works:
DNA strands pass through a tiny protein pore embedded in a membrane. As each base (A, T, C, G) moves through the pore, it disrupts an electrical current in a specific way. These electrical changes are interpreted to determine the DNA or RNA sequence, enabling long, accurate reads in real time.
This not only eliminates sequencing biases that may be introduced during a PCR step but also provides rapid results applicable to sequences of different lengths. With ONT we can sequence long strands of DNA and RNA while maintaining high accuracy.
Applications
Long-read sequencing with ONT has many applications and therefore many ways it could benefit your projects and advancements. We are currently offering:
- Adeno-associated virus analysis
- Whole genome sequencing
- Targeted sequencing
- Epigenetics
- Transcriptomics
Curious to find out more about the possibilities of long-read sequencing or do you have questions about what technology to select to get the best results? Contact our specialists to discuss your needs – we will guide you to the right results.
