Our main objective in developing MagicViewer has been to provide an ideal framework for short reads alignment visualization, genetic variation detection and annotation through a user-friendly graphical display. MagicViewer not only supplies a versatile alignment visualization system to allow users much more intuitive and straightforward to access to large-scale reads, but also provides global/detailed genetic variation annotations, which is customizable for biologists and bioinformaticians to analyze next generation data efficiently and flexibly. If you have any comment, suggestion or question, please contact Huabin Hou or feedback below directly. This will be an important step for our future update.