Introduction
DNA sequencing has come a long way since its discovery, and now we have several methods to sequence the genome of an organism. Illumina sequencing, PacBio sequencing, and nanopore sequencing are some of the methods used today. In this blog post, we will compare nanopore sequencing with other DNA sequencing methods and see how it fares in terms of performance and accuracy.
Illumina Sequencing
Illumina sequencing is the most widely used method for DNA sequencing. In this method, DNA is fragmented, and short reads are generated. The reads are then aligned to a reference genome to assemble the sequence. The advantage of Illumina sequencing is its accuracy and cost. Illumina sequencing can generate billions of reads at a low cost, making it ideal for large-scale projects.
However, the drawback of Illumina sequencing is that the reads are short, typically between 150-300 base pairs. This can cause problems in assembling the genome, especially in repeat regions.
PacBio Sequencing
PacBio sequencing is another method that uses longer reads than Illumina. In this method, the DNA is sequenced in its entirety, generating long reads of up to 100,000 base pairs. This makes it easier to sequence through repeat regions, resulting in a more complete genome assembly.
One of the disadvantages of PacBio sequencing is its cost. It is more expensive than Illumina sequencing, and the throughput is lower. This means that it may not be suitable for large-scale projects.
Nanopore Sequencing
Nanopore sequencing is a third-generation sequencing method that uses nanopores to sequence individual DNA molecules. In this method, single-stranded DNA is passed through nanopores, and changes in the electrical current passing through the pore are measured. This allows the sequence of the DNA to be deduced.
Nanopore sequencing has several advantages over Illumina and PacBio sequencing. Firstly, it generates long reads, up to 2 million base pairs. This allows for much easier genome assembly, especially in repeat regions. Additionally, it is a portable method that can be used in the field, making it ideal for environmental monitoring and field research.
One disadvantage of nanopore sequencing is its error rate. The error rate is higher than Illumina and PacBio sequencing, resulting in lower accuracy. However, this issue has been improving with newer models and algorithms.
Conclusion
In conclusion, each DNA sequencing method has its own advantages and disadvantages. Illumina sequencing is ideal for large scale projects, PacBio sequencing is great for a more complete genome assembly, and nanopore sequencing is portable with extremely long reads. It's important to consider all options when deciding which method to use for each specific project.
References
- Goodwin, S., Gurtowski, J., Ethe-Sayers, S., Deshpande, P., Schatz, M. C., & McCombie, W. R. (2015). Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome research, 25(11), 1750-1756.
- Mardis, E. R. (2017). DNA sequencing technologies: 2006–2016. Nature protocols, 12(2), 213.
- Rhoads, A., & Au, K. F. (2015). PacBio sequencing and its applications. Genomics, proteomics & bioinformatics, 13(5), 278-289.