Which course is better between M.S Software Engineering(Integrated course) and M.Tech in Vellore Institute of Technology?

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M.S is better if you want job settlement in abroad eventually. M.Tech in VIT is also good but not that much for MNC jobs as much for Lectureship. If you aim at being lecturer in engineering colleges then MTech is your best choice. Else MS is your course.

which are the colleges in south india that has ms soft ware engineering?

Friend,
-ALTHOUGH,MTech in Software Engineering would land you with better options of getting job instantly through campus placements,I would personally recommend you to go for a MS.
-MS now has higher career opportunities,especially in Foreign countries.
-Also,the chances of Growth through Technical lines are now growing limited,and those through the General Lines,though take time to come,but have an expanded lot of opportunity.
The call is however yours.
Take your time and choose the best.
Good Luck.