Starting in 2005, several novel methods that rapidly increased sequencing speed were developed. Although many different methods since have been developed, we are going to look most closely at the second-generation method developed by the company Illumina.

Second-generation sequencing is actually very similar to first-generation sequencing in concept, but its primary advantage is that it reduces the amount of space required for sequencing. Although definitions are not rigid, we will define second-generation sequencing as a method which uses a "wash-and-scan" technique. In this technique, DNA polymerase and nucleotide bases are repeatedly added and washed off in cycles, and optical detection is used in the "scan" phase. However, this can be wasteful of expensive chemical reagents. Second generation sequencing is still very resource and time consuming. It has a high error rate and can often only read short fragments of DNA shorter than first-generation methods. Its primary advantage is its efficiency with space, which allows it to read millions of DNA fragments at a time, leading to a rapid reading speed overall. (44)

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