Why Choose Nanopore Sequencing - Advantages of Nanopore Sequencing

The adoption of nanopore sequencing technology is driven by its unparalleled advantages, addressing numerous technical challenges effectively. These advantages encompass exceptional read lengths, direct sequencing of DNA/RNA, genuine real-time capabilities, elimination of the need for substantial investment in sequencing equipment, scalability (portable or desktop sequencers), 10-minute library preparation, high fidelity, and the capacity for high data throughput sequencing suitable for large-scale genomic analysis.

Ultra-Long Read Lengths

In the realm of nanopore sequencing, ultra-long read lengths align closely with the input fragment sizes. This type of read length remains unrestricted by sequencing equipment, allowing users to modulate fragment lengths through the employed library preparation protocols. To date, the reported DNA fragment lengths have exceeded a record of over 2 megabytes, with the longest direct RNA sequencing read length reaching up to 26,000 nucleotides. Extended read lengths provide a more definitive approach for aligning and matching DNA or RNA sequences, enabling the generation of high-quality, more complete, and continuous genome assemblies. This advantage is particularly pronounced in plant genomes and genomes with large structural variations and high-level repetitive regions. Analogous to assembling a puzzle, longer read lengths simplify the assembly process.

Direct Sequencing

Nanopore technology, rooted in the principles of electronics, grants us the capability to directly sequence the raw DNA and RNA. This process bypasses the need for DNA copying, chain synthesis, or nitrate conversion, thereby preserving the integrity of base modification information (such as 5mC, pseudouridine, m6A) while saving time and costs. These pieces of information, along with the raw signals generated during sequencing runs, are retained and can be analyzed at any time. Thanks to the application of nanopore technology, we can achieve direct sequencing without the necessity for PCR, avoiding issues related to amplification biases, and simplifying the library preparation process.

Real-time Sequencing

In contrast to the traditional sequencing approach that delivers data in bulk after the completion of a run, nanopore technology has ushered in a dynamic, real-time sequencing era, providing results such as pathogen identification within a matter of minutes. During the sequencing process, DNA swiftly traverses the nanopore, with the rate increasing from an initial 35 bases per second to the current 450 bases per second. Each read completed on the array requires only seconds for data analysis, eliminating the need to wait for hours or even days. Users can assess the quality and status of the sample early in the sequencing process and terminate the sequencing once sufficient data is obtained. This rapid turnaround time from sample to result holds immense potential in the future for the diagnosis of infectious diseases, on-site dynamic monitoring of outbreaks, and other disease diagnostic applications.

On-Demand Sequencing

In nanopore sequencing technology, users have the autonomy to control sequencing time, location, and the number of required chips, distinguishing it from traditional sequencing methods. For instance, the single-use compact sequencing chip, Flongle, is suitable for rapid quality checks, genome experiments, and small-scale targeted sequencing. The portable sequencing device, MinION, weighing a mere 100 grams, facilitates sample sequencing at any location. Desktop sequencers, GridION, and PromethION, are equipped with 5 and 24 or 48 sequencing chips, respectively. Each chip can operate independently or concurrently, supporting real-time data transfer. Consequently, users can select the number of chips based on sample quantity and initiate or halt experiments as per data requirements.

Cost-Effective Sequencing

Traditional high-throughput sequencing comes with a hefty price tag, requiring investments ranging from hundreds of thousands to millions of RMB to initiate. In contrast, the startup kit for nanopore sequencing currently costs only a few hundred dollars, inclusive of the MinION sequencer, two sequencing chips, a library preparation kit, and a cleaning kit. With the capability to sequence up to 60 gigabytes of data, these two chips provide a cost-effective solution for genomic analysis.

Flexible and Scalable

Oxford nanopore sequencing devices share a common core technology, allowing users to easily adjust experiments according to application needs. From the compact Flongle and portable MinION to the desktop GridION and PromethION, these devices cater to a spectrum of experimental scales. They are applicable to on-demand sequencing experiments, ranging from single trials to ultra-high-throughput projects, providing rapid, long read lengths, and real-time direct DNA or RNA sequencing. The library preparation process for DNA or RNA in nanopore sequencing is straightforward, with the quickest library preparation methods taking only 5 to 10 minutes, involving the addition of sequencing adapters and motor proteins at the molecular ends of the sample.