What is Massively parallel sequencing?

Second-generation instruments read millions to billions of fragments at once. In sequencing by synthesis the fragments, with adapters ligated to their ends, are bound to a glass flow cell and amplified in place into clusters of identical molecules; the clusters are then extended one base per cycle with fluorescent, reversibly blocked nucleotides, imaged, unblocked, and extended again, so that each cycle adds one base to every cluster’s read. Reads are $100\text{ to }300\,\mathrm{bp}$, usually from both ends of a fragment (paired ends), with an error rate of about $10^{-3}$ per base, and one run yields up to $10^{12}$ bases. Third-generation long-read instruments read single molecules without amplification: by watching one polymerase incorporate fluorescent nucleotides in real time, or by threading the DNA through a protein nanopore and recording the ionic current, which each sequence of bases modulates in its own way. Reads of $10\text{ to }100\,\mathrm{kb}$ and more span the repeats that short reads cannot, at a higher raw error rate that consensus reduces.