Dye terminator sequencing has long been the main method for providing sequence data, but it has the disadvantage of being time consuming and expensive when analysing a massive amount of data is planned. A revolution in the sequencing field began at the turning of the 20th century, with sequence by synthesis methods ^{1) 2)} and there are nowadays (as of 2011) many different platforms available for high throughput sequencing. These methods have in common to parallelize the sequencing process, typically producing thousands of short sequencing reads at once. The Wikipedia page on DNA sequencing provides a rich historical review on the subject and many scientific articles describe the differences among the technologies ^{3) 4) 5)} and compare the expected results ^{6) 7)}. The high throughput sequencing methods are also called next generation sequencing, second generation sequencing, third generation sequencing or massively parallel sequencing.

A few QCBS members have used one or the other high throughput sequencing methods currently (as of 2011) available. One example, that uses a AFLP-like and a pyrosequencing step with a Genome Sequencer FLX (GS-FLX) System is detailed in a specific page High throughput sequencing at the QCBS of this wiki.