M.A.Q Viewer
Maqview is graphical read alignment viewer. It is specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. Maqview is nothing fancy as Consed or GAP, but just a simple viewer for you to see what happens in a particular region.
In comparison to tgap-maq, the text-based read alignment viewer writen by James Bonfield, Maqview is faster and takes up much less memory and disk space in indexing. This is possibly because tgap aims to be a general-purpose viewer but Maqview fully makes use of the fact that a Maq alignment file has already been sorted. Maqview is also efficient in viewing and provides a command-line tool to quickly retrieve any region in an Maq alignment file.
Maqview is based on OpenGL. Installing OpenGL on your system is the trade-off of getting a better feel and look. The following screenshots show the two viewing modes of Maqview.
A more complete instruction about how to use Maqview is presented in this page, which also comes with the maqview source code and binary packages.
