Once the clusters are generated sequencing can begin. The approach uses reversible terminator nucleotides. They include a detachable fluorescent label and like ddNTPs are blocked to prevent chain extension, however this can be chemically removed to allow chain extension to continue.
Before sequencing the two complentary strands and you can only sequence one at a time so an endonuclease digests one copy of the strand. Then a primer is hybridised and you add the nucleotide bases one at a time and record fluorescene and chemically cleave label in between each one.
After the first round of sequencing a single round of bridge PCR can be used generate the other strand (after sequence just created is melted away). Then melt away the first strand and sequence the second one to get the sequence at the other end of the fragment. We expect these to map about 500bp apart on opposite strands as this is the size of the fragment.
Sometimes a third primer is used to sequence an index. This allows different samples to be distinguished, meaning we can sequence more than one sample at a time.
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