In addition to microfluidic flushing and washing cycles, as also used by the other NGS methods, e.g. the semiconductor-method and the nanopore-method, the Sequencing-by-Synthesis method is based on very precise and fast XYZ-optical image scanning of the whole sample area.
In advance to flushing the flow cells, the whole genome is put to many shorter pieces by the shot-gun technique. These pieces are then PCR amplified and split to single strands (oligo strands) before they are finally attached to the bottom of a flow cell channel. From here the stepwise recombination of base pairs starts vertically and each recombination is indicated by a fluorescence signal. The base pairs contain four different nucleotides to result in four different fluorescence colours.