MapView: visualization of short reads alignment on a desktop computer.

We introduce a new visual analytics tool named MapView to facilitate the representation of large-scale short reads alignment data and genetic variation analysis. MapView can handle hundreds of millions of short reads on a desktop computer with limited memory. It supports a compact alignment view for both single-end and paired end short reads, multiple navigation and zoom modes and multi-thread processing. Moreover, MapView offers automated genetic variation detection. MapView has been used in our lab and by over 10 research labs worldwide. http://evolution.sysu.edu.cn/mapview/. Supplementary data are available at http://evolution.sysu.edu.cn/mapview/MVF.pdf.