First thing you have to look for might be if the Masters course is aimed at people that already have Bachelor in Bioinformatics or at peaople with a general Life Science degree. For example the course at the FU Berlin (were I did my Master) is aimed at students who already have a Bachelor in Bioinformatics so they will start with advanced computer science and statistics topics. The course at the University of Potsdam (probably also Hamburg) is aimed at people like you and starts with basic computer science and statistic course (they also give an intro to Perl and R).

Second there is a wide variety of different focused courses. For example the one at FU Berlin is (or was as they have changed the curriculum this year) focused on genomics and system biology and the computer science and mathematical side of things.

So I think the best way to choose a University will be to find out what the focus of the involved research groups is and see if that fits your own interests.

In some cases there is also a possibility to combine a Masters and PhD program like here .

I don't know anything about bioinformatics in Germany or how their Masters programs typically work. But, you can find a short list of professors offering bioinformatics courses (and possibly accepting Masters students) in germany at ROSALIND. If it works the same there as here (North America) then I suggest you think as much about the qualities of the potential supervisor(s) and whether their research interests you as about the university. If you take some courses or self-teach yourself any programming language you will be ahead of many who have started a bioinformatics graduate program from a biotech background. Commonly used languages in Bioinformatics are Perl, Python, R, Java but also C, C++, etc. If you are a beginner I recommend you search this forum. There are many posts recommending books, online courses, etc. For example, here is Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics..

This paper named "A review of bioinformatics education in Germany" might be of interest: http://bib.oxfordjournals.org/content/9/3/232.full - though it is a few years old now.

As far as job opportunities go, if you wish to study for a PhD there are several world-renowned bioinformatics groups at EMBL Heidelberg. If you are interested in a PhD after your masters course, it might be useful to contact a PI you'd like to be your supervisor and ask what masters courses they recommend or often take students from.