NGSView is a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. The screen shot above shows all FANTOM4 CAGE tags on chromosome 1.
Different features (quality values, SNPs etc) can be visualized. Above is a zoomed in view of a promotor region.
Other features can also be visualized, e.g. time course data (above).Please cite if you use NGSView.