The Four Powerhouses of DNA Sequencing

DNA sequencing has come a long way in the past two decades, revolutionizing how we explore the complexities of life. From understanding disease pathways to advancing personalized medicine, cutting-edge technologies from Oxford Nanopore, Illumina, PacBio, and 10x Genomics are leading the charge. Each of these companies offer unique tools that cater to different scientific and industrial needs. Dive into what makes each one a standout in this dynamic landscape.

Oxford Nanopore Technologies: Real-Time Sequencing On the Go

Imagine carrying a sequencing device in your pocket and performing genomic analysis anywhere, from a lab bench to a rainforest. That’s the power of Oxford Nanopore Technologies (ONT). Their platforms, including the MinION, GridION, and PromethION, use nanopore-based sequencing—a method where single-stranded DNA passes through a tiny pore, causing electrical disruptions that identify each nucleotide in real time.

ONT delivers ultra-long reads, often exceeding hundreds of kilobases. This capability is a game-changer for resolving structural variants and repetitive genomic regions. The portable MinION device enables on-site sequencing for applications like infectious disease tracking and environmental analysis. Real-time sequencing lets researchers make rapid decisions—ideal for clinical and field-based studies. However, while ONT’s technology is versatile, it’s not without challenges. Accuracy, though improving, historically lags behind competitors, and throughput can be inconsistent depending on sample quality.

Illumina: The Gold Standard of Short Reads

For years, Illumina has set the benchmark for sequencing accuracy and throughput. Their sequencing by synthesis (SBS) technology powers platforms like the NovaSeq and MiSeq, which are staples in laboratories worldwide.

With error rates as low as 0.1%, Illumina’s short-read data is trusted for applications like clinical diagnostics and population genomics. The NovaSeq can churn out terabases of data in a single run, perfect for large-scale projects. While equipment costs are high, per-base sequencing costs are exceptionally low, making Illumina a cost-efficient option for high-volume projects. But, Illumina’s short-read sequencing (150-300 base pairs) has its limits, especially when it comes to tackling complex genomic regions or assembling new genomes. Hybrid approaches often pair Illumina’s accuracy with long-read technologies to bridge this gap.

PacBio: Marrying Length and Accuracy

When accuracy and long reads are non-negotiable, Pacific Biosciences (PacBio) delivers. Their single-molecule, real-time (SMRT) sequencing technology is celebrated for generating highly accurate long reads (HiFi reads), which are ideal for tackling complex genomes.

Spanning up to 15-20 kilobases with >99.9% accuracy, HiFi reads combine the strengths of long-read sequencing with unparalleled precision. PacBio’s ability to detect DNA modifications, like methylation, adds an epigenetic dimension to sequencing projects. Whether it’s structural variants or phased haplotypes, PacBio’s data excels in delivering comprehensive genomic insights. The trade-off? PacBio’s instrumentation and reagents are costlier compared to ONT or Illumina, and achieving high coverage can increase both expense and time.

10x Genomics: A Multidimensional Perspective

While not a sequencing platform itself, 10x Genomics transforms how researchers extract value from sequencing data. Their Chromium platform partitions DNA or RNA into droplets, enabling downstream library preparation for platforms like Illumina.

By linking short reads to long genomic fragments, 10x Genomics reconstructs haplotypes and resolves structural variants. From immunology to oncology, Chromium’s single-cell capabilities provide unparalleled insights into cellular diversity and function. The ability to integrate genomic, transcriptomic, and epigenomic data is a boon for systems biology. That said, 10x Genomics is reliant on external sequencing platforms, and its linked-read approach has faced competition from emerging long-read technologies.

The Final Word

Each sequencing technology has carved out a niche, excelling in different areas of genomics. Oxford Nanopore’s portability and real-time sequencing are unmatched for field applications. Illumina remains the go-to for short-read accuracy and large-scale studies. PacBio’s HiFi reads bridge the gap between accuracy and long-read capabilities, while 10x Genomics unlocks new dimensions in single-cell and multi-omics research.

The genomics revolution is far from over, and as these technologies continue to evolve, so too will our ability to decode the complexities of life at unprecedented depth and precision. For researchers and biotech professionals, the challenge lies not in choosing the best technology overall, but the best technology for the question at hand.