DNA Sequencing Comparison Paper

Comparison of Illumina and Oxford Nanopore The discovery of double-helix model of DNA structure by Watson and Crick in 1953, contributed to the framework of DNA replication and its role as a genetic information carrier (Heather and Chain, 2016). DNA sequencing was first developed by Frederick Sanger, is the process of selective incorporation of chain-terminating diddeoxynucleotides by DNA polymerase during in vitro DNA replication. Many improvements have been made to Sanger sequencing later and have greatly increased its efficiency and accuracy. The improvement of DNA sequencing instruments, detection mechanisms and bioinformatics all contribute to the development of automated DNA sequencing. The human genome sequencing projects provided a

In 2007, Illumina/Solexa published genome analyzer platform based on sequencing-by-synthesis and was used extensively for second generation sequencing. SOLiD sequencing which based on sequencing-by-ligation, is another dominated SGS platform. Second generation sequencing technologies have similar general paradigm, they need PCR followed by cyclical rounds of massively parallel sequencing. However, third generation sequencing(TGS) is sequence by real time, negating the requirement for PCR amplification (Heather and Chain, 2016). TGS can produce longer read lengths in a short time, make it suitable for full-length viral sequencing and many other biological/medical researches. The first successful single-molecule real time (SMRT) technology was introduced by Pacific Biosciences. In 2014, Oxford Nanopore Technologies (ONT) published their first product and attracted a great deal of attention over their GridION and MinION two nanopore

Illumina paired-end reads permit it to read genomic fragments up to 5-10Kb in length. MinION can read tens of kilobases and has the potential to perform de novo sequencing. Those long read lengths allow MinION to span genomic features of interests such as secondary metabolite clusters, repeat rich regions and operons (Lu, Giordano and Ning, 2016). However, its error rate limited its ability to outcompete other SGS techniques (Laver et al., 2015). Main error source of Illumina is substitutions (0.1% - 1%) while Oxford Nanopore’s approach have higher overall error rates mainly caused by randomly insertion or deletion (5%-40%) (Goldfeder et al., 2017). The errors generate by Nanopore theoretically can be overcome by more